view PSM2SAM.xml @ 1:34f9e847dd4e draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit cf9086847f3153e28b697b5f4b0da1a677eb165a-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
       #if str($input).strip() != "":
          --passedPSM="$input"
       #end if
       #if str($scoreColumn).strip() != "":
          --XScolumn="$scoreColumn"
       #end if
       #if str($optionalUserInput.exonAnno).strip() != "None":
          --exon_anno="$optionalUserInput.exonAnno"
       #end if
       #if str($optionalUserInput.proteinSeq).strip() != "None":
          --proteinseq="$optionalUserInput.proteinSeq"
       #end if
       #if str($optionalUserInput.proCodingSeq).strip() != "None":
          --procodingseq="$optionalUserInput.proCodingSeq"
       #end if
       #if str($optionalUserInput.header).strip() != "None":
          --header="$optionalUserInput.header"
       #end if
       #if str($output).strip() != "":
          --OutputFile="$output"
       #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>
    <section name="optionalUserInput" label="Override Default Exon Annotation and Coding Sequences">
      <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" />
      <param name="proteinSeq" type="data" format="RData" 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" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" optional="true" />
      <param name="header" type="data" format="txt" help="A text file of SAM headers to include in the output file, usually corresponding to the exon and coding sequences used." label="SAM Headers" optional="true" />
    </section>
  </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.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 SAM files from confident peptide-spectrum-matches (PSMs).
</help>
</tool>