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executionsTemplate.xml
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executionsTemplate.xml
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<scheduled_executions>
<execution>
<class_full_name>com.era7.bioinfo.annotation.FixFastaHeaders</class_full_name>
<arguments>
<argument>XX_sequences.fna</argument>
<argument>XX_sequences_header_fixed.fna</argument>
<argument>XX</argument>
</arguments>
</execution>
<execution>
<class_full_name>com.era7.bioinfo.annotation.PredictGenes</class_full_name>
<arguments>
<argument>XX_proteins_tBLASTn.xml</argument>
<argument>XX_sequences_header_fixed.fna</argument>
<argument>XX_PredictedGenes.xml</argument>
<argument>400</argument>
<argument>false</argument>
<argument>30</argument>
</arguments>
</execution>
<execution>
<class_full_name>com.era7.bioinfo.annotation.RemoveDuplicatedGenes</class_full_name>
<arguments>
<argument>XX_PredictedGenes.xml</argument>
<argument>XX_NoDuplicates.xml</argument>
<argument>XX_DiscardedGenes.xml</argument>
</arguments>
</execution>
<execution>
<class_full_name>com.era7.bioinfo.annotation.SolveOverlappings</class_full_name>
<arguments>
<argument>XX_NoDuplicates.xml</argument>
<argument>XX_SolvedOverlaps.xml</argument>
<argument>102</argument>
<argument>XX_RNA_blastn.xml</argument>
<argument>XX_sequences_header_fixed.fna</argument>
<argument>genetic_code.txt</argument>
</arguments>
</execution>
<execution>
<class_full_name>com.era7.bioinfo.annotation.GenerateFastaFiles</class_full_name>
<arguments>
<argument>XX_SolvedOverlaps.xml</argument>
<argument>XX_protein_nucleotide_sequences.fasta</argument>
<argument>XX_protein_aminoacid_sequences.fasta</argument>
</arguments>
</execution>
<execution>
<class_full_name>com.era7.bioinfo.annotation.FillDataFromUniprot</class_full_name>
<arguments>
<argument>XX_SolvedOverlaps.xml</argument>
<argument>XX_Annotation_Dismissed_incl.xml</argument>
</arguments>
</execution>
<execution>
<class_full_name>com.era7.bioinfo.annotation.RemoveDismissedGenes</class_full_name>
<arguments>
<argument>XX_Annotation_Dismissed_incl.xml</argument>
<argument>XX_Annotation.xml</argument>
</arguments>
</execution>
<execution>
<class_full_name>com.era7.bioinfo.annotation.GenerateGffFile</class_full_name>
<arguments>
<argument>XX_Annotation.xml</argument>
<argument>XX_Annotation_GFF.gff</argument>
</arguments>
</execution>
<execution>
<class_full_name>com.era7.bioinfo.annotation.GenerateCSVFile</class_full_name>
<arguments>
<argument>XX_Annotation.xml</argument>
<argument>XX_Annotation.txt</argument>
</arguments>
</execution>
<execution>
<class_full_name>com.era7.bioinfo.annotation.GetIntergenicSequences</class_full_name>
<arguments>
<argument>XX_Annotation.xml</argument>
<argument>XX_sequences_header_fixed.fna</argument>
<argument>XX_Intergenic.xml</argument>
<argument>XX_Intergenic.fasta</argument>
</arguments>
</execution>
<execution>
<class_full_name>com.era7.bioinfo.annotation.gb.ExportGenBankFiles</class_full_name>
<arguments>
<argument>XX_Annotation.xml</argument>
<argument>XX_GenBankGeneralInfo.xml</argument>
<argument>XX_sequences_header_fixed.fna</argument>
<argument>XX</argument>
</arguments>
</execution>
<execution>
<class_full_name>com.era7.bioinfo.annotation.BasicQualityControl</class_full_name>
<arguments>
<argument>XX_PredictedGenes.xml</argument>
<argument>XX_DiscardedGenes.xml</argument>
<argument>XX_NoDuplicates.xml</argument>
<argument>XX_BasicControlQuality.xml</argument>
</arguments>
</execution>
</scheduled_executions>