From 2ca12d1f9ce73d776eb8c7040af87b45458578cf Mon Sep 17 00:00:00 2001 From: drosofff Date: Fri, 19 Jul 2019 16:43:12 +0200 Subject: [PATCH 1/3] add a index-metavisitor.md --- index-metavisitor.md | 76 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 index-metavisitor.md diff --git a/index-metavisitor.md b/index-metavisitor.md new file mode 100644 index 000000000..aeb053b70 --- /dev/null +++ b/index-metavisitor.md @@ -0,0 +1,76 @@ +--- +layout: subsite-galaxy +website: https://metavisitor.usegalaxy.eu +subdomain: metavisitor +gitter: ARTbio/metavisitor +--- + +# Welcome to the Metavisitor Galaxy instance + +Galaxy Metavisitor + +{:.no_toc} + +[Metavisitor](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168397) is +a user-friendly and adaptable software to provide biologists, clinical researchers +and possibly diagnostic clinicians with the ability to robustly detect and reconstruct viral +genomes from complex deep sequence datasets. A set of modular bioinformatic tools and workflows +was implemented as the Metavisitor package in the [Galaxy framework](https://galaxyproject.org){:target="_blank"}. +Using the graphical Galaxy workflow editor, users with minimal computational skills can use existing +Metavisitor workflows or adapt them to suit specific needs by adding or modifying analysis modules. + +The Metavisitor Galaxy implementation comprises tools and workflows that are maintained in +[ARTbio/metavisitor GitHub repository](https://github.com/ARTbio/metavisitor/tree/metavisitor2/extra-files/metavisitor) + +# Content +{:.no_toc} + +1. TOC +{:toc} + + +# Get started + +Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take [a guided tour]({{ page.website }}/tours/core.galaxy_ui){:target="_blank"} through Galaxy's user interface. + +# Training + +**Want to learn more about Galaxy? Check out the following hands-on tutorials from [the Galaxy Training Network](https://galaxyproject.github.io/training-material/){:target=_"blank"}.** + + +# Available tools + +Tool | Description | Reference +--- | --- | --- +{% include tool.html id="blast_to_scaffold" %} | blast_to_scaffold Generate DNA scaffold from blastn or tblastx alignment of Contigs | - +{% include tool.html id="bowtie2" %} | Bowtie2 - map reads against reference genome | - +{% include tool.html id="psy_maps" %} | Visualization on a geographical map with psyplot | - +{% include tool.html id="mean_per_zone" %} | Plot zonal statistics from a raster and shapefile on a geographical map | - +{: .table.table-striped .tooltable} + +## GIS data handling + +Tool | Description | Reference +--- | --- | --- +{% include tool.html id="gdal_gdalinfo" %} | [Lists information about a raster dataset](https://gdal.org/programs/gdalinfo.html) | - +{% include tool.html id="gdal_gdaladdo" %} | [Builds or rebuilds overview images](https://gdal.org/programs/gdaladdo.html) | - +{% include tool.html id="gdal_gdalbuildvrt" %} | [Builds a VRT (Virtual Dataset) from a list of datasets](https://gdal.org/programs/gdalbuildvrt.html) | - +{% include tool.html id="gdal_gdal_merge" %} | [Mosaic a set of images](https://gdal.org/programs/gdal_merge.html) | - +{% include tool.html id="gdal_gdal_translate" %} | [Convert raster data between different formats](https://gdal.org/programs/gdal_translate.html) | - +{% include tool.html id="gdal_gdalwarp" %} | [Image reprojection and warping utility](https://gdal.org/programs/gdalwarp.html) | - +{% include tool.html id="gdal_ogr2ogr" %} | [Converts simple features data between file formats](https://gdal.org/programs/ogr2ogr.html) | - +{% include tool.html id="gdal_ogrinfo" %} | [Lists information about an OGR-supported data source](https://gdal.org/programs/ogrinfo.html) | - +{: .table.table-striped .tooltable} + +# Acknowledgments + +The authors would like to thank Bérénice Batut, Björn Grüning, Anup Kumar and @galaxyproject + +# Citation + +Please add the following when using the [metavisitor.usegalaxy.eu](https://metavisitor.usegalaxy.eu) Galaxy portal: + +*The Galaxy server that was used for some calculations is in part funded by Collaborative Research Centre 992 Medical Epigenetics (DFG grant SFB 992/1 2012) and +German Federal Ministry of Education and Research (BMBF grants 031 A538A/A538C RBC, 031L0101B/031L0101C de.NBI-epi, 031L0106 de.STAIR (de.NBI)).* + +More information on [how to cite Galaxy](https://galaxyproject.org/citing-galaxy/). From e456b28c1b4cd27be440603234bb6f9b22822fa6 Mon Sep 17 00:00:00 2001 From: drosofff Date: Fri, 19 Jul 2019 16:49:55 +0200 Subject: [PATCH 2/3] add metavisitor logo --- assets/media/Galaxy-metavisitor-logo.png | Bin 0 -> 23194 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 assets/media/Galaxy-metavisitor-logo.png diff --git a/assets/media/Galaxy-metavisitor-logo.png b/assets/media/Galaxy-metavisitor-logo.png new file mode 100644 index 0000000000000000000000000000000000000000..c4c41088602e8c2c4e4e2d11a4a2fb3bf467ce8d GIT binary patch literal 23194 zcmeEuWm^18Sn?9tE9XJD)`}t zYVi^L9nDEj*A;yI%+oJ8NtO&R@Ig{HX&pCp$9Ha?rY@EcPft%y8wXogb5kcvPDdB3 z445bx1VRIme=VWmmHBVU(~Cfp7-e~t`EwmJWn1t37dQxIx~(Sc#m+^nl~IY z`8sbCn4~puIOOnc{*>2`(Y`7S!;yn8OlY+Cc-JXTM5N~F;n~Re*Pn{&J1k3tnRY0< zW6MA$kpV3XM-r7b%nNRR9|Hcwk(BF~7-D{UfO<@(07ZLx^l|3RiTr<`Z2yp``t;>E z>jKGsc>g`B&f84--&0^R=KS|$eYPyu4F5eclKTHo_5XCOK1zL7Ry0lHM*OTP4wtyI z?}SPVr?mCoPF@M}TyrSZF+(5~$0!i_uy@_;(AY>Eysy?z`z4nimK+sMJ+|YAk4jr; zko(^r7B1S!y-a6>mc+u)iq$kB5cN_v{*G+6Z&_Xfq>^eO17-|i$=FXDFNb7h^a913 z%S~oE>N0fYTbUPv3X*b854a4jj;TT?HgjjpCo4OlAx+dMUA~niQcPip+)t;ekPaV7 z=kq8MB0G(a>4QBP4QluoRALp0c0Vde_u&fsv4YtelwrstD+PrCw>YN@;uX~dMUa#W z%EOcm!%<84Mv?aMeS8%Y0;KOuE}erwVq*m4@Or(-005t)kBApJP}@rsueU5s;U3DRXwSP|j*>T&sU zRc~>>02M+1;n7D*NfEwJ1WU|>gj-nb3_lQY<{y=DxD3V7++fL&#rNHbk`9+@tx7$K zN-f_lBZa}Cp`P$(#O*HC7Y7TzThK6^M=P;Lln?S;%^p0xG#1M*YNqyC$TflzPh8{0 z*G=VGbS)dr%V#8xex94uOBh9R9O=H`irBryrfA$C6OcWc#48iT$vK@Hw33lQW>WsL znc}OQ#tk<KiZ@-UAHk^j*=x(FT)X;W*dLYlVH9l94A*CdqXjKV5vM{II3(`V zoD~rzQMgy_+3+Kg-eXt+BhTIntxS7pYIb%@ovIF!k!&-KSD9@K5sb; zkbMjbqpw}i+t?5#k$>s36*94(z{nmKGL9fhfa9zgu5;>rv??K&i1@+Ok1|p!mCN|Y z)<~*9B{FRxMIF`3vtDMdxjk>rE4)2eoD|z2yVlBtuG%tY+Pj#Dv?R2($({w(owGNd z-hIEmB1ENm$OkOsyQ|B8a*;iE-xXf_&MHT|-t)RqLx^s@44vmBJt-+PEUa7T#Qt!( zqZ2C_N9{M-z~!*W0#3ojdViibq6^*b2g-peOb2`#>HSBT*0e(anYh1AB{v6 z&2l9F$qL<(!$s{OEDv2qYEhFmQI*E2c-dw+3uoPC&*2{KGlGdox#8vTYis283b~ap zvf1GtgVx+BRuWnnn=0|t@3{t6a&EN zYevuzBIq~0%~Ssf>cJb&0K~iBU4}6A+na*Er6$2 za;e44o{cSPduRqC^Fy&h0rMcKm$0MBeMax-v5M<4+<7Sku`Eu`o&urUYr$9xHs;0% z`hPj44}Z1k@{UmRXxd&2Bj)F#r}$-ycw)`X&2?fGyyoB2b+%h-odQQ+EtBPy5Fv_8 zrSpML9qu%OK23V`@DIXnw`%1u*cKY21CyB~JMGRd)-f!yq8+h*TWuO6&OiiG+9cvu z_l`ekP-oR}-BUD3A_FZaClj#e(ZH)BvbRmy_X-`Xl6L8CxM&yslDnbd# z-J5-8=S6sQ`y$0(0ed9ab`s-_4GjZD@LCjZkU~uEjQEF}9_9{$4r+59Ybr`~_n85j zOff84RyY$9Cr<%{nZoBJ{$JOd+%9t=U79USB=$HAb+(QUlAWntKeD}y!WE!!3$3bw zicmgYUMJY%OXCQMc9YwSgLvy1#$)CX!s6?kSG=1G)PFE3pEY_&?HFaDLLJyS*#Ali zd47KoUC8CBSAE1T^Dyk*k)kzHm3Sy$vRBpfP7BDya39r~@A1dS*F!7wZIyIa)s9;k z@v&|jI9y}Tb8V!*?2lD3E`eP%qvX@VzP_1&L7eWcoYRz;j3eF-E_e8{(w5RR+OwAw z;4wHkvn}N4KStY`vfsO&zH~2%z!kM5tq)y6gnacC3y-%c&x0)vKwSp3s$Fl%AY(`f zA$MwKuSpZX<@!-i>9+8Ge^=qUho?DWjo2a3F9nCIt=YVp^w*mL>Nh)MN+7u}#{Qws zYIJ=#g}oCiG~O&kMiq&83cai`E6;bUcO8=id0k-PvMMe4%{r&UJ&J4Idsph_K_XPL zbH-dXUtv47Fwn;wrfe`#&kJxG&sfrOS8Eq|Fx;yBG44yce3&`clhFkaux5*wMLc2u z_PHStaI}P6x1*nq>MQb?k6mgF2k@E;oJCMB(q|@1byN_VOcAu>VWb*&`ezNM`!7Ns zHo~(pl7!wk%=i)&p~>t}%O(icD3_8iet)po$QZlkg-@}fXtv>=Y)yA@B zW^`l%?+cwQPFmD;I`x|zX1|$7xb$4nCJlvUW>SEcLL(?R^YCrl`n8i2x1^*b4jI|| zM|?cIkeV89CyKxOW6$QknahR;CYkc4$7g0n|NN;$5+g%EK+tW%O>lz%>FMd|e+c{V zAzvaC`Kv)oZJhWs$-AVqZ203py5M4bw1dm=gMZZ(aKBiV;kDWgm&2Ij?d|Dn+H8cp^gtN@`VPr8LCx4BWJ9&=`7?K(=4+_~_{A-!{D0w6L&f zo*W29K;gC?qY0-^3Ut)=Tx@zjg|1hrwf3?7@J9@}kk=7SER|T~#y}iB7uVvd}bAsR;Ak}z zn~sSInN73%L73juW6v?)GsJ2RLR}d`d2ujq7{3I=2cn3Qx;bso!4JeV(tkXxf;9 z!%9T6>~K5sexNLEu~A5x53bpJyuQh(c$YeROpW(7DPW1*Io~(jqvzql-QC^&s#W>r`}oW4-^spze`nppl9{YF|Nb?< zKH1V~^QcrT$oS1og7GmbO3J{1;^Aro8-s)!;(v2?Jot6xIWd<}U*=2K`1ttMZ@yQ0 z9v&|)4p-uun}srkoZ&?e@4rvyv&<)rgTwB&KaCkDdV>0Xrs_Z~@JF?bq!5?m3%Z@k z>h6Y*9=p)x?}rAMr`0P%@5}eDXxz9616&Tx#|pVc$#ol&uB)7i z#-5cb2tJdm?xz$$LnxoXV)Kqcj5X~s!HMxMY*N58@n>;{$ev<$|ElK$=9&gYNS7fR zQ+wpdCF^0|$Y0Z|%@p1R>l|tn_rK8Jm;M5z+gqpIj*sR4)PGcn_C@p4&{vN2Dj_oF zV5R?h*OaK*{Q~}ary!1vB*h#F3F)boD$dk$M8#5y(20o|u6-39wR>Uy>x+QSH!~!3 zboBOsM{+?2lb#Tyrw>pC-Z`HgED%dbNJO4Ha+4e_IChyXwYqP4#QeQJ{rm0x6x$Q_ zb$q`C|H{FEQ>)r2Ch*}JB@`L+dk`E#rqS(40}M4_MMl^DxxO~t;7ZcyuMwK!lEL@- zYQf&6G^)$zR9}>9s1}h&wk>O@=C;PweHo;n6(~(}&+7S7$|R>+@h2}Y!^`}&yQc&; z+odmNj8!C`Z@mNL3R~yl8dI$?s_T(aK0t{RkMEDkodd>M5|P&#)QDCdhwo3fmg@ng zed&^(cf=$1`jkb<4MDX*koTOyQQHiB{(e`++`MOtUnL(r^ctWTfsl|86aLSB!@=~O za?qu87e{bSzxVbc?4`-bC)PM`$lM(dP!In8ec>)N`0H1HzI4>ljB()FLDPy%1Qz8Y z%yp*9@M^at=WhK}{R=qXQBl2Rn&o$${3N5NI`!7L5BHbG(PRR{rA0`4x76Xgf4Lyb z$JXucD>AF+@33k@MVp8*9!5Jd<&$X~D2Oi&E`$|6nmp|C>8Qdkhwh8WNmo59 z;ks-w(~j8Qc=}`PQ6Y2-*zF~G^|2G1=yu?IrVK>*+?{q@OSOPNyDRR5nQCS*!`({8C^}%?6k2UcdQ!77(y5p4usK`)zDY>3W^_Q!Y(Z*Hy|WFRpt zk+r-{Oin@@*+Z(SFoFP#Fs6DlSAI#XLixHU?61Y6@eTfdkA1c(RP4+WS3SujlXp1# z=cjaS(=U9u26b2_R1h$BWJN>l+v$E`C*zC3AGbFhYN`N%a~wsHqWe^y%=%VQ(l`KA}=6t zpj6q2d@b;uSJ`D_A5tq-^qU>`k>lB-!=T1`&U5_v#MLD2j?Ilr6*6;2HE^7Id}<*{jwZ>f3- zx5J`P4r4aQ$Phj--?=I=3Nmgz#%ZRs3KdXYmENFLo=O1r(To9lFGukww0HgrfIdS^37ng*A@urkaF~u+ON2rcdUZ(}5!?QAvm^K&1 zSnIub9=>+EMkO!W<7{F(souGQhv;_VZ3Rz+kH6s}E>kehZhN7`l++=UR|m^<>6%Iv zZ}q$81v*Qi+%FaFdH{l+5pi_?Oy}eAzi}%Wff=-W;R5b(@y0E<^lgF6$JmR*tfg4F z#IU(KD|+^kV=jMpY;W7wa6*2#r^0UoB!60m=E6=sMj)_-_G4^#n$x6XR9%ACLRS`S zJ4^6HIbieDUjjy@mNwA7>bci<#DC_E+`@RG#Y?i%=5wu*0V(kEh@d#0$X*0HZ{Onl zrZ}E;L1@&Yw9cV2y^Syl2j{ov&`5hH;In&_qj9&hN%?fhLjm>3q8pQud_CiEtd3G` zfFr1r{R)h_s{cZ5en(L0O{Yo=@Z7TEx+n2}2QOsMps%Dp={=JqK6;uo>GwL{Fll>}CCP zZ_tmxYdY6tLz$qE)5-k5&hI7}c%>Br-WV`R*pc+@xMflgt;> zrG=TFz9Iu23Iw6hN&^I?t-T-x%v~S!zI~t+)ZITf?1CS%IMYjK%%xz=5wM+p4KRk& z?jOd~n@G@TkJfs7gl?p_kwJ&@+*NBPh!kha0mtzb5Q!#c+z;jnRmIK;AT+$ZcxY&7 zLjE`Piae7Qx^-h+TNNuDLwDDwxTK_?e#E4(3Q_LBI&U2oT}Q<@;}&nDD)pQ410Ns0 z8g~VxAMlHrn*^Is zH?9~Ip_GG16&XAWvD#-JhN|hT?+mzw{qz17wv%(K1ZqF*DxsU$PB)F($<6I@bEVq^ zsx&*He~8O&I+U{_=l|d_#=#z zDAVGpRXt2}siQq!9$_E;RWGu-Jn5^YMf5xCbWwyWsy{?30;|Q%ew@{_`>}XwV|~5G zqtbSN)w5P%Bc%6U0trFr6yX zPGsjg|1xxlXJ;S6I;Qs zGAY3=80n4>R%3st+GhKiY1ZqxItXRqf{ZaE5z;fIqTGlZBLw|Ehj7@(Hp)p&ihIMv9ASU@Hb5 z=AT0W9}oMv5}Ydt4J~tLE{Tn?{7(0;pkf(kj6O#izh-C0n!~Vla_a$$LTL3{LRD`B zc3UR*3x~yKo%}6T`W#(d-886w>&T4bQY)chn@2mC_Cv;`oD^d*@1x`1)qj3xMRI?1e_#v$W_^~DBV*SIRkDgf-#dej* zW2#1ojqi6KwH4Or^n;@8;J~eT1$+}w7aA$Y;e23i%+AX5!M1;@W;ebJ7zM3uq|#)v zw?{}`9kPJ-8vam_V={Ne{4?<9k)-kW~Wof^lr zE^}@_%?p=o5oddm(3OTCrXssC$bFLxX@NHt{~q%7qy+Eqonj1DybkOEC?Qhr&d<-s z!NpxWVdVpbdLW)wDjBtsq{yRXWgTq5>Gm&I+tBgz{TUv=E2qh7V`{P(VxGD5i>Kh_|()0fY6?rb>-&QuK?HPtL8vesHb#{Fe!w_N~;}Tzedb2 zC~&@9@}vg^29x|nn8Mc8Oe{+z&~62ZI1P5D$v^&~cz=u* zoBNs&wdC3885*(O-{DlvjEN+Taj}C4R_--T9A01ipIxf#_iqrE;d_%4fDUJw&P;xs zk=i5VnE3CPCfEdsr#7FieR$n~>Gj`B-mZ6FB2XkRZwiBalL*F!ti}m=icE3KcjG(8hTJ@$v!KQM%zPW|58(s7m%RsA*I?4ujr4t$EX7+!l@gM+^#v{#Z zIe%t9Z)X3S^*Eh0zA9vJaIhPgJIAY`;VbtZ|7LN^wNniTZvjtuQa9+F>m669l9-g$ z3b{O=(BgCb#@Bv+ex>$q!jwP;fe@*sj+n~rSaTh1^#ZpxgfOumgNXya6$r?!m#cr`TnQ0LN@7AS zID(2j6NIaugx{otj3f#(5^EnZq@`zvl5#hy(~O^$13zE4Zy%@T`aT$XUtaPBr?3&f zRfFID-3pNTc~w0i3ExeeDl_GPj#Z{zZS>DMP#y|!@czl~vqWxi=t2$Iw-?K`xpWKO z|JM6v7M`DDp381?z&zl*GnR+&Bbqd{KZeZ$88LvU+JJFetVJj%oB3nV&M%r4u?e>O@jIY}iSb!RLZ)IE#e;|E8MBTI;{ zp?rlMtnI(C6C%`jZqJ8rHY~jv=Y!OijdE zqnj!F)k`HPpiP)rRcEzWv0m#KE=47aaF1yof@CqXwU$x&{uevr2*17zWhAncfj!CltYwTePf$TE!fMY z0x@UTY)JLRt7dvKi~xRQA;GsTXGMRtv`ZWIa~=X}8^J<4He_3RrTcEb3Fmj#tA`yp z#?NLGXWm3TNyNdGQ;;W=N-2bQb7>_dXh+ffRV&gTx@V+1_d*q^#wFG7JwI8KQQ_~* zm!X*y1N#Y^c!)if& zonlh?pS_(^WLP}D*{_zW^yo6Vdj5A*q>5(<_`;g|v9&jKRC7qIGY#k4Fr1`O3AtqL zFG^D_*d&$hhIiR?!}8FVgt@Da0>_xAwR7<<$;NdD98BvM9}Ib(&pmu|qNPGQ#11=N zXrg^r2=^YdUbQneelEj~Ig4;E*~$otjkJ;dAz9br%&1agj66r`a$dIa&=A{fe-UX( z(K3gN8Wmpnn#2BVG^^B8K5JQjJ_W6W$#U({-HC!l(2Sm+?c^=;XD|J{H73N49}r4k7}(7xSja?_IwAyWO3sc9dYdq6J`hX${JHWt)OM;Ye09~N>9$l~`+B$a-#@#; z!eoQ6FJ5s4>qozVMwBw8vUE(#ee*`wKI^5nA#Ngr$hF1(qGt18YaBPPEm~x$d^Tp7 zS2WPkHzvme-aZmRoMeyPl)FqBtEC&#OpJK(kskLk1DYz|2@p?_^%y^w9@AI1D?uRa z5wMAfcYK5=o|-q$Tag!WA^@%naJfs6+)i}ocZ_v((nj`?;TDi-86%^fg{)4K{rLk< znLaC-v9R|^;krLtLq>}V<>CSHPw=JF-rh zczAW>M8PvrfAGtS&V`EcdY2O4N~)&Hh(7Et-2%X_fIEX7=6j6BFc&>D8M5e=&d`uc zWJw`v#|5w11Lv@x%NPghy$6KPHF&V;t|t0T*jhXyv+L60oq#L1m*VR!^@=&iGUlO$ z@7&>=j?>xB+tlhVMksW7>n0U+QjXK`>6sxbNy(6P|92J^EQx2>0BVA}-M`usI$oqm zEPB0}g!=56Yn!nG)L(Uo*Sa=IRmhW|NKlY!sFQd^V!}VjDm39!samfyJ>+f~6Q|nX z$cg{84X`Lp#PaTb7dbw=fJ8en{pxZ!!bCE%T9+8eA0~Dj(R|CH$yr!3 z#E1uVj`SAO$ktTeL=ukv_TrHffrt`E zgKrBH8Ct|r9KY$*nD!#?ocmx<2;qS8)jO6a#bY(q$sN?l6F?gahvcwr-g zf+UgfO0LXvGEy(GzI00A@LKWl`)4;0=XIS52P`OTVjm)%MtVaW;q*JO+^Pc*nFj9} z&1y>p#?H=v!U=V%IV6n&i@3n3!-w;dl9>3fRtU2^-o-(Z_E`%H#3PAAvHo(J*6F$4sK2!9Do%r-q-WxHHy(b7YE(%Z0BFz3aSQy9biw zcU)~r7xX|Ub_S`=ipJm3i#}h2fvs^iS{8xn3*8~{m`9ec02uCzx>tHEu zy&t5${&?W$DFp>q!&t`!u4M7Oy$F5>>X1c{_i+=;m5EbcQuLEjJQLxQ*g8VL1?vuX z0WK6QCSZGed;QGDdrMKlWp9!-6+avJ3?hsC8zY+&`0B8x3Zo7(U^s9Z+VZB?nDwLI zc1`^GbF`h|Xm)pXtkdrGjqdm*pQhq4v3t`)(9gHpj!GS;BAfR7W|H6YK08AjX1F;f zv7wA@Eom;eNCh_`EA2l+C2*ULiMr;NjPL?(737c_S603lsUpOiT;E!O)wjG|PJCT+ zPA>I0#5L9>PHy+>dj@&SS1nXBL4-GR3PGQS{+eVyaDp{B_4-%lap`+UwM;ZNR8rs~ z)hT)~n4}I1ax7UAOZU^`Aga)77%s8}0K$-CZFG3}`%n@y;jPcs-w|>fx-Dz~9?LEa zEgQBj@91wUthD7?=76rwSYFw>Z+=0n6qx6IBtQ2_6arF3Bwf_ly@kXycb-2(6L7VU zeFd)ye^(j+IWS;C4bqrn`AZ7HKJKr@cfcMAq65AMP<60vON9M2z&;q`F$oFD^WGsv z417SDec$L$0Eb6ohG4eZ>E~!2}OTMl2y&4XD91=;LCe^DXq7?CX4Y&@FK~R&15G%Ew70V^8 z)YjY1U;)oh(_%u+#$f4{R>G(Jk5A_2_V(wirXCZ>=qX4`fS(s}Q4jw6<`VIq(S^*` zK0m&*ZICE~7k1Zk@W#_;klq=@Bv24h211uNRl#Whf`gQx1%}eIE|)#w{cmD5Ksx8F zW#spdm@UKca-Kk8&HBgp+kddu19vh`^qCAf;=!sQP?2m`Qn(nhWqMFT^I&(V^`mhJ z`js#0Rol^(bF7|K9ug!zgqog=0Bdm(=D9&V*12pnfs?-=EJ|&(_dF z7A65uDtIDwxb!l~EgpjO^axQz&qEZ7zJGmN@N|~ffra?=rN6U8B0xw*7}~plmhAWW zxu761aLZl;UF807bJIfl5!+AR-O-cV6t`B!>x!~mG}R9lFDL?B1@x-7u5o> zBmiH#^3TZZ)B>{8Mzp7?-W4N1wiu@SVUI~Un>JdokgO6^d)+zd0mwR70Rt;zqM~D+ zzbAa0+73_+V-fUQ$Y#Hs(^{4w2+F=Z_*BC1y>`zkE#S6lwgS29-qAWD`h3vAt;+J6 z{2Xyu;$)WvE$Y)J=a*oS3UYok?G_8IoPiSBouogr)=C(@KnJEH8| z-(+7Vr2Ky#Yr`I~@PnHFW5Ju1$FIGeAP8ylV2&K7&X^OxLV9Ad)IqdobTY#`(m!QW z=#}$8vznwTJKt#kEJkMIMB^WDo{uKgPrCAes{oQ9hONYJJWRa@V}_X}jazr#mg4TfS3J2Z6_%1gpH*-L1*ibxA~a;8E&a z+J{(98L-l$Mh6lb!GbAzC#Xt8A63E zDs!c_zU@M74A5BfKx)C^%sPLYEa*(ZkBu3&onWO{IlyjN0uEE{FN#8=u;N3UTQ$s$ z3T&FKcT&ScVQJautRe-oq_9|2VpW9vH|<(qGvL>(W(l{T;4Y{iRxttiyw)9zurpB- zS8)MTYPr4r%Dmc=&~o^YCZM~R>UKar3v|5#MFSu>WWYPnU+crk;YAyFA?@cKTtr+|vV+7R z5^dcBt6O2A({>Hrqj8m4NC+;!hp@&0HOsL#FeOO3$e;0u6&<;gQPzjb%t5F3x(8ln z8?q<$WAHpDwWG8|iBB6lN%uo`D`ji};!4)MfMGHpW9nkM%jM;Hc2Jt*SdQDJhev~t zZ_yeBB>-Mz=_Wgz?~cVwV-v`IT#s7-B`tWR75+!{O08;&>n{-+uRY^_74G#Wj;0t5 zc%TWZC3uBdY{>?tk10f6?qajOJ|P9$00jSLzxz-4%ofVTM$JxeKn`%-r2^`?jP z&|}Fmjoc=SKtR6eN;r%+OVk^WSvC92odk|cM1-6=@Qw$_pi8hQOWme-RCg($6ji3R zBbd!I0s$Qa_bT--+Zue0u#_RnEvX-X!_kv-kG`K^_!O@Fe(lwN(|C}W^X%04G_SK- zkUtK~_4ctu)Rav#Vdf3Nzk-P6KCNLIp=J`u5u=?ala2FlIGOBMZvlIrGOaNL9s`r3L(pK$$AEVwY2}{ z2sXhTaE=@kwp`fSWR>Th<@x7~9Ql_y7mz7Tof4k6Q>4du%+7)nNdv(^SgLVGP48@+ zomXXL#{Z$a@s^uu+9*n6>Kn1-yL$vpU?!2;)p>(V&tmp-7MpoP-pvA&b?&sld!p|x z_>Jlb7M~T^M~7F~C0Rj5i2xj-&F?->Dq^^TFg-arY;sZ~^`;64%s^|U5IjT3%gY1e zehHi8$^CwH7ab#Gzq3@jP%L}u5VH=}7Z`$tz}BN7^X=>WL^-6ERYjdp?Zj8})|(id zWdb2G{-4HjJf$xGpqT8l=|9G=G@)HPo_(-fGRtwuJw}P{+? z4M~^xNTZQvW$?T15tFmV8Ga@P3cK@GhkmAF#$F#YanO(d1xBmOO0~Q6R0fO`p!0!r zqKvqqm|%NuF68+5*cyoKpGLLASUrOhM^9h?X6SV2{j3Ni6etV}?P)GSvH}6M>+ANR)m($dUcLdssHXB>Kwb3YX+sEFxsqWiG#GzjY z?Wkg+&)R6l8?m~6*7)0S^-E*w)O1#itV`U4hUY&`4hfb~jpyb#{2pYIf%8ZQ zxo?4m%lfCpiB1eOr+2a$esd`_Rsk7-Wyrzek`E6QcX#d9c&kg|G<- ztbIU}0*MXu^>czCb&1p2XQ=6Iq(G{kj~#38Hw*C|QX;sk_RLfEvwLo-kdHgSHaTcj z_wE-C5z+S1>(75cUULmFQ}&B1kSaJBkPt3^KUHSE*!)d#<|ZVOJ_nPGzxx?id#+C4 z@|yw~Oyh`E9^hoLUHC8NNujh~F8i(uVNv^^;i_b^_!HZ`1?GVJ{`8ao0#15-R@TAf zXtq)HfZ&Q>Xsi3a8DR8Rpcz>j?<)iAkDH0Yc{WzO8M8ISfV<~+M=*YM$skm)tzD%> z0`T?KgtJ}@})yq4Ck$Gu{>T>*QLy4ZY(N~W{lHdXpM%Me8PLgpgM+bZCklcz3 zV2dH>aBx5BT3EOqA|FLGN-aD}Tbmi9;A@e#uI0R1vf}R!nN*4Tk1+}5g3A1mx{=VJ? zGJU5CH_+HmpMqt~eS>%Z6h-xJCIQ_Y2>16l=TcyO|Iud`$jn8)H16;r1TnEbfFmeA zAG87|`%P1oJ?1n5w&-fpP)XScy-C0wLE@am%NNV=-~w1v`OKF-TxXTTk=n-0y>BS} zC|nY96CChHd<+{@nwknji*h-WEyFz(w!!e@kp$H28|{|LrX8#na#(V=Ry9K7{4am< zL~HW7e~<8!OSipu`<^v+MjpPERs9&JwJ&Sz^wE~ac;1K~ku-l$&UAtDWke~${6G?FvK6O%u82pF?w@BZj*$^43X2YwzBKyFZBRpj9)k!`iHWK-rD&S zk*t+-&Py`)OSte7B6gvtO1S)hoOkN^3Jj!-jNta25s;L`em+Oe%{L9{MXyXhV`%I- z&|3m?NI}<4hahF&nD7fX30L&I+RWXw=%+1rfFKdlp%}ti=0Qwd>qIYVdIQ}2-(|Rh zXYl;<3kR66sc-MjXrDqADBJ=m5>gwtV z$;q2)#=!HE0lRMy+fOVMEA=Lxx695e+tV8j@$EFwcoi$wzQo4|fmq90II&STXz&Rj zLJT4=>!l^xY-g^M^)~7t#)|2=VtCRrEDchKYfGLh{dJ>I{hi~d$S+`HQULVxn0`l$ zrg({mfP&QrQcz1bcMAEN(V?w>@oVSNO0WSyPF|{Zf>Ny$k}_74$ar87Vgk8iKA0Yt z*Oz|MklM8rdw+as_0nELsP-hdbUmv`&LDJQWCE0a6EGTfP46=|Ev1Op-1dd`s?Hdf z-vN1c&mG;69fW{^wjJVpBLp1vAemx-Z1jnW&D{VP7O3qX%K9MbekOgjMZb5T>`F_LckiUhdS;Z+%>bz5as#imz8IY zA6&#!w{XFj+|xk<7LEbigoP1r-S<=zHZ=UTqS8x|KqJRa2L;_3)65rGNQY2+Lz;&*CTy!m_(}nHdRYL92s$Q<)9o9J;@`WT3s+n=KBsYt5+tk0B=BpvXyoxFh}A^ z&N}m5uDne~A>_P9OwRJD1{bKQ-mY|U{TArtFCAWsa`LG^SR1IQV7>dD`Kh||1|5`= zUJ$*&p`wDFbjU`N1aoy>!OO-{^yoWw5T;pm^C{)wCfDj*IwsDP&;+eCXlYHHIOQia zfy~eA!Fqu)s36(urlT)#IC{wb&IbgaM4$f|{F}uXKRX#~jeM5tGi)Hrs2IC~VGs_Z_Ss5Hjv#y10YJmQc^v3{ zG+T}3DD@S6yCYr25ArxPq$iY3BAv3+1Y%$U$=%pdmnShpiUHFMx( zYyQ!6eOsE#_=EGgGQcyA@VFeqURWGg8~EU)V`k8b4$OvhMoK=vl(<=-1cR4lzE+djMcR=^~jK1My3V zX=xv$qcNm!=&ITT`VT5#OKt2fkDP|BuPU|J|D;xfNxN553O_0$QzFifup)k4W!YLR zX-{n>eCPW9`o*taguGpm*B-uWY5QHLBkY<<9!4#3@jk~MZ+&Bk=1V>-OxqEW&+&i1 zTkr%YsDm5=F-U5BVhq4U2>~Deh8ps-NO)?RUm{D7T5T_ z70yz*_<<)2WQ|Bdc7olJ6&CM83tibZww@F)z0rJWWa;6IjDk`C!gY~nTZ%6GcEWyn z_!Tw7qAE$ni%SK*y9i(B2SqGZezv27rHP;qF$S*7wN27!Vm5+n#{c>OnQ!*(xv%@Um5 z%yE4>jK*85r^;Aeg=4r%MZ_>bK&vL}{79wSjPw3F35AAGs0y)X+5xp{PE4g=F4E+s zwOJH3l^PkV$WmwzA{Fo*Qc@E+M~cM{s88Ewg1geA=Vf2W`fL76W(V1D^yL7G;yG%` z;a~6t&q6L*JaKp(%kR5UCcd*e!^riygRILi}KwP|aA+!W`F)_+_uDe5#BK%}AiYsv`?CicUcbju5gh&}H z@#jSxi9?Y6<3A-%l_-satyzo8Dus3i8;wCfi(ac$*(z#?enLxVT8nGZEHpGN+sUTd zZDLtlL|b5Cf@rpJa{s!40GqL%vTlg`%_T`t{L75I7=O&>(=$f-FdzvH26hm01ad(T z%R8W@Ks!)8_l#2Wgl%|G6Uv)dy>f7|+FPOw7TpR^1e~8x8Tu5P12z%MbdET9E6EIK zAlDLk?#cYY)PSrzm6L$qlg?4cPyA>j{qD~(gkradI( z#8s3c=5*HQ(u+cA8c*Y|01XZUI9}p-@lcOkrCM=XS8-Fuirv~q5+aHmFqYEFj=Fc60d#dq|gj#%t2#sTM$tk z0#Ytq6dELVS7h=c_djvsnw~1edkg!?1uCFAI~@J+kYo&I6ELbw@ew;j@LRRT;dK^R znyyC=59mu_ZyE|%J*_l%HtU|QT&&6vE|?hF zm?S|<*MFnIu&LQoW|!jLB0!t6IUmlG+V-_zsO$-{yo0y8RvnreVnHB^4L2?_5T^jR zsfT-4 z`Y0on74Mn8Al}|@4XYX5lQ>V75)fOeF(1IHUSt;%BC%g+JRk08F9NA0Fw+s9zkd$O zY$Bs#jqMDl==r4j&U9r)enCHSDBM#Q2Akq^b!57^>E(c_t)Y=TqKT`Jn359CWBw!8 z_3v-5i#e;eO%A)#G2Yn&zzKBT{z>{YWdo@3Md^V;3LD^E4u?nfe+oZMxZ4)w=RZwK zp#lf`F^)mr8jM*8gF!#70|P7X+TWZ{Zk30jUEBP~lVa$#C3V}?&;F_Qw~O}5qxBjl zVV@Wge%NboX4`MLTO!xVAgs7$Az7Q&J#C}0?pA9t7;3qNT~ncpIAnKbEvlqr`BhIQ zw4&F^FmjP8Eb zVAHA8id!icRc=|ypV)m0G{*hYQUw#gXS);MEQavhV2h-cdJU4mV#%G@wJ_w8$NMue z0Z^{pqbtauGB7fFw>xY6Jc;$XhvZHWq{6GcQt1&4*DB`qHx zJ{XIuy>;ELuN)hDgF(uRc)93`9dLiHZ2;sy^q@) z+TeKv(9HC}B$uM#qe@6xHnQCCXkn?|kJ(PnJ{v;lH3mAmyXG_{hIx4>-iKp1;Y`Zs~Of-qBDl)$8^}aQ+s?03`X-p8OACCz z6X>C-EywUK=w3S3Gv~M{aC|!__qBJ8VE&k{eQ#Tk45%c!H~F)vtz!~(cI=JCxNb*X zqq~;J zuXu@Q9_^XSI(F3httt>Ky)}!FdvqXS9cRszfL|e@z3s-qv%Jsf>O7O)&M`#X1ca73yrDr^WGn!75*$AJ0pL$ z@Rim|V&*~l+c1gK)Of=A+!)e%N@>#`|m@gef?1*5%_2ejb`r+l^d6E zfa#X?(>y8g4B%|QgjL@1HV=TwVITLl7GDDwj*5!P6%gFG?t0^lTBAF&^O$IIwb)7}h%L5q*3 zkgk4wHARbajcGMt3Ik-{eAQl(Y9flE(7Z|*7^ma{;x}YwgA2g&Y6qNvP0TIitwq*L zIf7R8-il@BVFmSIRXV26c2yly`b7gyv;)fM5)64A=%R1{(w~RHU|=*bhqLgvwOs?l0Ov>E_PH6H17Z?@EiRg5>l0^ck$4ju+gfT?gO~))UY>bk zb_C&>u+R63yMQ?dTwi$eldnfyGG)oQ081ni+j%@1LO{rS`cG^0cDskz$sK?rd2Y<8 z7wm4G1PK4B2SFwdJe%bHXOui>dAoBIL#Ux=wSH~3Jmb(OD6l)dLJaZ&=lPRwV-K{o zk22_&OPcAp-YJ=}k09Qn1jc@i-I~x~XwLaNnR}@XtiYJ-6cHCvJbobffS<$-1lcR+ z?NE#?uw~KxkJT0qg5=9WY=7G@vrR1lxU5AjOqK3=iw=zMzQ*AMU*Rnof`_>OtB&p%$LHNo#-t;{l$2h*RBd0s+s=i8mKI z9>sE>tQd}|y?-*_t1}V=AZS4wry+6yTVDZay&@3zvP`;ARz=^t&Y^_xOzG*Lm7mHW zF5248kB$MaAbhJ&IV1t)8+0z;CLdx#mDavJWh~s?Ykn2_p^tD!D~bE}>X)Pe+hx^| z)6o#%X1;NkS4&M0OaO1S9;v~&-hS!7I^GfLFL3-P(X}7I9oU4f()=z5YadwQxu9VaT~F=bH;NG)zB~Aj?*d4>FqQJFWlz(#e5(!>EGGVzDi= z7#z%bI?mT=uJ;2Q#dwL^+#|YA333vnE}3dae=q&)diyiU&9ki5#C8Fej&Aaf&fEom zB9*!qERQ~vm}`tendOb_xtsj1p^FiXYdU!ED`CGx&x)qzeyxbVxihHwV+~69``~Wg zRDZpHmL;pW_VBu{P$&^kAQDZ1axgYFCT+K^+y%5iF8`*{oG-2lta5T-2?U6|;S#5B zZU_jvApm+5FdchOCh%q%QYO>9-n%GS%p$pxeeQ$aO(@fGz>!x4P+aUCRmICEi84f<`#&a3y|enmdd^oty5)u?I}LGHYK6~S_IXS;gt-t+f8)xz5U5clno zTQFI{_EoI}aaIpUL@+{c%yul0;&ujIFO+|(QOYOI5{*;6vq8EVMhz0)9BoA=YZ*D% zrY>cpwL%K`4RW_thKl+aaYhwe$hyv33Gg^3)6#jVzd%AOu}255x&rzeU( z<2ackWGzjrKz!A_!XY+b>%J#G$KFg>L}Ynk%{3vWK4UQSRscbc%ise1az1QXb>8biO)h8aS-_u!F+!*M2S53wWiS`ST zHL#Z2{Vv8S(Q}4HefV4zEcgA>4Rw_r*Qed@Z@YO6 z=!AuZ6_5m}rY#yd9_m#1?ZS`*fGXFB964$7g-6y33s->dfwk$?LyOjSgJEy0bk zygb2z7GY}j))Gk*Xe|;DZ2c}A0}?UsOwfKtii#m7SW7Oyl>FYx=Tk~O8L)~LTNv9J zLHMSbkx}l(#s<%eu@b&f1j*djH$Lct$ zSCUp@!jFCYbn`tM47!I@EQVM2c~EzU8=ju{1IdvoJ`}nj_by?CnI7r=tI=(j5mtnQVi6)Gf*G_GYP79 zz2>@e`O&~iWRCN7>lU0bOt8I_ChLbaDSe!<7V!lriXuRZnSXhvj$0aY04EYKg7uU^ z3!gSF$IAMZT=jPsxzoolHo3aj7UY z?{b)qsxtHIxzS>a&7?Iyu;fIav6{vUOdc2SkXzn;XOSU<A76_1QghR#?E}LmXCj z5vIc#N-T#$o#{f&$!r`P`K{+tGQq2uubYhp@s+#DKVa;a!ao52kqZzI0e?TYgV-XR zvYJ^h;|>Cj<~8n_H?-bg>2G^@J>0es0CQ>ba))NM7|g{o8@x3L1-ns27r@5mSz3Nn zRMcH>C)ButhNdRv>v5LvRvGxxQZ0ACC!80HJtH^vWQ zP=5Pbz2GbAvJXeg@;fQ}Wbj^ITgK2bCp-x{abtIqK5re?T31XF-clK<9UY54KfS70 zCiDCFEmki&G2cq`YgNW9e;0EatQ48y9o|i9?#rGq?CD7<-fq`qr+v`~9~GgNE+^4` zMS$-d%>d2v6YPa3ARSop@uL#(GI$yUZ?A(|XFot*M9O90W-Kr4izj=P6%vW8 z^k0A4lPPNo?0OMHAv<{+> zYFDRA3k&s}or_!$2#d0uQ2>pwv$GdfRvNWL)OeVP3J56AXL!W{_tyyaK;|{#+XIoU zg3OhP0uf0@PGP&}AHEsyv7zRTPx>|G_w9My{PQ3Sj0(QGsNQ#8`+hURqMGA*BX^$! z;~qERvP=$ihoH5aRdY355|$JEWBq@N>1#H0Uc>YXSnoGUE_aV^yEu7A5j&Edi~q{K z;!*#=Zc*nLH5Dd{dm=k~oc30}v16RXchfN*9f8VqrO{Zu@o=fnXa9W_8K$e6T`^l1 zkdz^ykyF0>mGca|=JT-IadG%nuRgW9-kS0f15-N{nIh(10Kisy+HHEc1_GPY&BY2n zP#R|GxtlVyzJ7R_Qr&3F0A^Wst+kZWqICCq=;<8wtonKxV-u6&j~}l&+YZbki~PtF z;21;Dpou9d1z;q%kzSAKkVvEvP+<$K8pdX3seK4A4*)sX+1qOp9NhFMp05lTEUzE< z&455P(1NDZdjkfMk}VQgCKNUFhQ$-;9tepMqrlv^XCsUo)aXJf2#5a4Pb*r zy9_|#j8UE&`nkR3eb~tw1poZPSs8m@i3a+eFlyWS9m?(uue`Ln5EFE(`PNB4eBN4< zF53jX?i-p0cWBnYaWTW1Jd?XC==yOLjD)|kkLNz!mV^@;@$}_uBvtm^mblt#AC3&3 zJ0ic_Lu4MNSqHdBF1k{DA`aJ*Uj}VjSM8v_+mwA3ryGWF1`j%v7^|+PZggARn17EScV|5m zybPX`&&Y_O7}huT4vMkZqm&^J{_rs9%K5kUW=Pz4EL!?tX}F>QNS6MmVYDIA&=3Nc z5@mqVX?nQ~i%p&+n>si+*mZza(uBG?o|KuH`GrN+4d%c0Z*g()(>8Mp3z2MM0Wix# zMMOmAbhC*m$>h^As^8I;QwQ0q%KBDiM&x*or1DKopWuhw43Z7XiJKq zKnafb#lbWG`U&(zK~!IspHT(Mw`8=o_dw`HN-1LR3DYqtS9%fyepft9zR1rV20%rADE15!dA&|G9!c(#hR~mc#=$;(O(CLVH--VrooCx+YTD=k&BRgNM!&rhZ zh*|O%rp()TBuh;Ts~b?hLC=u)j3m#23lTgW(6C#9` zbuGzV7{t~Ivy@=*4_zAt$G?H%o(pe}Za5x3%3dTtvhyDCCvT(MX5y(;A9JJ%8*S-r zVgj^f#n_+jSllFSo=yTH7`~YzMDebomb+G~23eFkn|64S#GuO!iP*<0%n*pocb^IG zI*kJ1Em}m>0B_Q;M`29qYLV;*+wa~?(NK!fyzcH|gXv`cnqwf_u9M#=&%Fyf6kTw8 zVe%i@I=0CZKJv#P3hicmsmH?!Fr=l+Ye%oNQlt3XD<~kLa9f9=)}}2Y#F8mL;tjNx zbIjUl2;`@EKT-vHIvc|~Zb7adOxrEs`}-W!V+j54M^j~m5Vv$5JX2GRRS5k>1C4#- zGOUN*SlF>%esScUWtDEoLIL2g*t0>(18~hj1W%)tQj2y=J}6b`;3cGN-#<0pIIww)EfO}K{TFuu2jei0-a zn!fu=X9Dq+Qu#Sob_4-#RLKDpW(a4t(avxA)F8&LdZ)N<#T-m<*4H^zW9rWM$^=DX$ZF}!2!Xtb=+BE`XX#Ay zeTYiu%-~sB)>(^b?gkI7AS>0d(ZF3Tf22zD^lr|S zqb~XXlm5?!IOI3ekQj4ySWy5?1yO&fqk>g>^6Gy8 Dx6N$h literal 0 HcmV?d00001 From fb21fd8577ef012fff52b7bdde93c16f1b45f65b Mon Sep 17 00:00:00 2001 From: drosofff Date: Fri, 19 Jul 2019 17:31:59 +0200 Subject: [PATCH 3/3] finalize index-metavisitor.md --- index-metavisitor.md | 43 ++++++++++++++++++++++++++----------------- 1 file changed, 26 insertions(+), 17 deletions(-) diff --git a/index-metavisitor.md b/index-metavisitor.md index aeb053b70..fd8501eda 100644 --- a/index-metavisitor.md +++ b/index-metavisitor.md @@ -42,29 +42,38 @@ Are you new to Galaxy, or returning after a long time, and looking for help to g Tool | Description | Reference --- | --- | --- -{% include tool.html id="blast_to_scaffold" %} | blast_to_scaffold Generate DNA scaffold from blastn or tblastx alignment of Contigs | - +{% include tool.html id="blast_to_scaffold" %} | blast_to_scaffold - Generate DNA scaffold from blastn or tblastx alignment of Contigs | - {% include tool.html id="bowtie2" %} | Bowtie2 - map reads against reference genome | - -{% include tool.html id="psy_maps" %} | Visualization on a geographical map with psyplot | - -{% include tool.html id="mean_per_zone" %} | Plot zonal statistics from a raster and shapefile on a geographical map | - +{% include tool.html id="cherry_pick_fasta" %} | Pick Fasta sequences - with header satisfying a query string | - +{% include tool.html id="concatenate_multiple_datasets" %} | Concatenate multiple datasets - tail-to-head by specifying how | - +{% include tool.html id="data_manager_bowtie2_index_builder" %} | Bowtie2 index - Data Manager for building bowtie2 indexes | - +{% include tool.html id="data_manager_bowtie_index_builder" %} | Bowtie index - Data Manager for building bowtie indexes | - +{% include tool.html id="data_manager_fetch_genome_dbkeys_all_fasta" %} | Create DBKey and Reference Genome - Allows optionally defining a new DBKEY and retrieves a FASTA file and populate the all_fasta.loc data table | - +{% include tool.html id="fasta_filter_by_length" %} | Filter sequences by length | - +{% include tool.html id="fastx_trimmer" %} | Trim sequences | - +{% include tool.html id="fetch_fasta_from_ncbi" %} | Retrieve FASTA from NCBI | - +{% include tool.html id="khmer_normalize_by_median" %} | Normalize By Median - Filter reads using digital normalization via k-mer abundances | - +{% include tool.html id="blastparser_and_hits" %} | Parse blast output and compile hits - for virus discovery | - +{% include tool.html id="cap3" %} | cap3 - Sequence Assembly tool | - +{% include tool.html id="sequence_format_converter" %} | sequence_format_converter - various fasta to tabular conversions | - +{% include tool.html id="oases" %} | Oases_optimiser - Auto optimise de novo RNA-seq Oases/Velvet assembly | - +{% include tool.html id="sr_bowtie" %} | sR_bowtie - for small RNA short reads | - +{% include tool.html id="small_rna_maps" %} | small_rna_maps - Generates small read maps from alignment BAM files | - +{% include tool.html id="ncbi_blast_plus" %} | ncbi_blast_plus - NCBI BLAST+ | - +{% include tool.html id="regex_find_replace" %} | Regex Find And Replace - Use python regular expressions to find and replace text | - +{% include tool.html id="sra_tools" %} | sra_tools - NCBI Sequence Read Archive toolkit utilities | - +{% include tool.html id="trinity" %} | trinity - Trinity (from the Trinity tool suite) | - +{% include tool.html id="spades" %} | spades - St. Petersburg genome assembler | - +{% include tool.html id="yac_clipper" %} | yac_clipper - Clips 3' adapters for small RNA sequencing reads | - +{% include tool.html id="vsearch" %} | VSearch search - VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences | - +{% include tool.html id="blast_unmatched" %} | Blast Unmatched - get query sequences that didn't get a match during a blast | - +{% include tool.html id="fasta_compute_length" %} | fasta_compute_length - Compute sequence length | - {: .table.table-striped .tooltable} -## GIS data handling - -Tool | Description | Reference ---- | --- | --- -{% include tool.html id="gdal_gdalinfo" %} | [Lists information about a raster dataset](https://gdal.org/programs/gdalinfo.html) | - -{% include tool.html id="gdal_gdaladdo" %} | [Builds or rebuilds overview images](https://gdal.org/programs/gdaladdo.html) | - -{% include tool.html id="gdal_gdalbuildvrt" %} | [Builds a VRT (Virtual Dataset) from a list of datasets](https://gdal.org/programs/gdalbuildvrt.html) | - -{% include tool.html id="gdal_gdal_merge" %} | [Mosaic a set of images](https://gdal.org/programs/gdal_merge.html) | - -{% include tool.html id="gdal_gdal_translate" %} | [Convert raster data between different formats](https://gdal.org/programs/gdal_translate.html) | - -{% include tool.html id="gdal_gdalwarp" %} | [Image reprojection and warping utility](https://gdal.org/programs/gdalwarp.html) | - -{% include tool.html id="gdal_ogr2ogr" %} | [Converts simple features data between file formats](https://gdal.org/programs/ogr2ogr.html) | - -{% include tool.html id="gdal_ogrinfo" %} | [Lists information about an OGR-supported data source](https://gdal.org/programs/ogrinfo.html) | - -{: .table.table-striped .tooltable} # Acknowledgments -The authors would like to thank Bérénice Batut, Björn Grüning, Anup Kumar and @galaxyproject +The authors would like to thank Björn Grüning and @galaxyproject # Citation