view customProDB.xml @ 3:7e078d4e40f8 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty

<tool id="custom_pro_db" name="CustomProDB" version="1.10.0">
  <description>Generate protein FASTAs from exosome or transcriptome data</description>
  <stdio>
    <exit_code range="1:" level="fatal" description="Job Failed" />
  </stdio>
  <command interpreter="Rscript --vanilla">PSM2SAM.R

       --bam="$bamInput"
       --vcf="$vcfInput"
       --outputFile="$output"

       #if str($genome_annotation.source) == "history":
            --exon_anno="$genome_annotation.exonAnno"
            --proteinseq="$genome_annotation.proteinSeq"
            --procodingseq="$genome_annotation.proCodingSeq"
       #else:
            #set index_path = $genome_annotation.builtin.fields.path
            --exon_anno="$index_path/exon_anno.RData"
            --proteinseq="$index_path/proseq.RData"
            --procodingseq="$index_path/procodingseq.RData"
       #end if

2&gt;&amp;1</command>
  <inputs>
    <param name="bamInput" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input BAM">
      <validator type="empty_field" message="This field is required."/>
    </param>
    <param name="vcfInput" type="data" format="vcf" help="A VCF file to create variant proteins based on individual variation." label="Input Variant Calls">
      <validator type="empty_field" message="This field is required."/>
    </param>

    <conditional name="genome_annotation">
      <param name="source" type="select" label="Will you select a genome annotation from your history or use a built-in annotation?" help="See `Annotations` section of help below">
        <option value="builtin">Use a built-in genome annotation</option>
        <option value="history">Use a genome from the history and build index</option>
      </param>
      <when value="builtin">
        <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team">
          <options from_data_table="customProDB">
            <filter type="sort_by" column="2"/>
            <validator type="no_options" message="No annotations are available for the selected input dataset"/>
          </options>
        </param>
      </when>
      <when value="history">
        <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" />
        <param name="proteinSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" optional="true" />
        <param name="proCodingSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" optional="true" />
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="fasta" name="output" label="${input.name.rsplit('.',1)[0]}.fasta"/>
  </outputs>
  <!--<tests>
    <test>
      <param name="input" value="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB.gz" />
      <param name="scoreColumn" value="Myrimatch:MVH" />
      <output name="output" file="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.sam" />
    </test>
    <test>
      <param name="input" value="Ellis_033_2700_261_07-unrefined-subset.idpDB.gz" />
      <param name="scoreColumn" value="Myrimatch:MVH" />
      <output name="output" file="Ellis_033_2700_261_07-unrefined-subset.sam" />
    </test>
  </tests>-->
  <help>
**Description**

Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files).
</help>
</tool>