view PSM2SAM.xml @ 3:ce09f1a1bbad draft

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

<tool id="PSMtoSAM" name="PSM to SAM" version="1.3.2">
  <description>Generate SAM files from PSMs.</description>
  <stdio>
    <exit_code range="1:" level="fatal" description="Job Failed" />
  </stdio>
  <command interpreter="Rscript --vanilla">PSM2SAM.R

       --passedPSM="$input"
       --XScolumn="$scoreColumn"
       --header="$samHeaders"
       --OutputFile="$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="input" type="data" format="idpdb" help="An IDPicker idpDB file to convert to SAM" label="Input PSMs">
      <validator type="empty_field" message="This field is required."/>
    </param>
    <param name="scoreColumn" type="text" help="The name of a PSM score to include in the SAM output (e.g. &quot;MyriMatch:mvh&quot;)" size="60" label="Score Name">
      <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 annotation from your history</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" />
        <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" />
        <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" />
      </when>
    </conditional>
    <param name="samHeaders" type="data" format="txt" help="A text file of SAM headers extracted from the original SAM/BAM file or reference genome" label="SAM/BAM Headers">
      <validator type="empty_field" message="This field is required."/>
    </param>
  </inputs>
  <outputs>
    <data format="sam" name="output" label="${input.name.rsplit('.',1)[0]}.sam"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB" />
      <param name="scoreColumn" value="Myrimatch:MVH" />
      <param name="source" value="history" />
      <param name="exonAnno" value="exon_anno.RData" />
      <param name="proteinSeq" value="proseq.RData" />
      <param name="proCodingSeq" value="procodingseq.RData" />
      <param name="samHeaders" value="header_refseq_hg19.txt" />
      <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" />
      <param name="scoreColumn" value="Myrimatch:MVH" />
      <param name="source" value="history" />
      <param name="exonAnno" value="exon_anno.RData" />
      <param name="proteinSeq" value="proseq.RData" />
      <param name="proCodingSeq" value="procodingseq.RData" />
      <param name="samHeaders" value="header_refseq_hg19.txt" />
      <output name="output" file="Ellis_033_2700_261_07-unrefined-subset.sam" />
    </test>
  </tests>
  <help>
**Description**

Generate SAM files from confident peptide-spectrum-matches (PSMs).
</help>
</tool>