comparison picard_CollectBaseDistributionByCycle.xml @ 7:08f69add4d06 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92

6:961236c5ec73

  <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements">
    <requirement type="package" version="3.1.2">R</requirement>
  </expand>
  <command>
    @java_options@
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"
    
    #if str( $reference_source.reference_source_selector ) == "history":
        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
    #else:
        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if
    
    java -jar \$JAVA_JAR_PATH/picard.jar
    CollectBaseDistributionByCycle
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    CHART_OUTPUT="${pdfFile}"
    ALIGNED_READS_ONLY="${aligned_reads_only}"

    
    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR
  
  </command>
  <inputs>
    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Load reference genome from">
        <option value="cached">Local cache</option>

      <param name="inputFile" value="picard_CollectBaseDistributionByCycle.bam" ftype="bam" />
      <output name="outFile" file="picard_CollectBaseDistributionByCycle_test1.tab" ftype="tabular" lines_diff="4"/>
    </test>
  </tests>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <help>

.. class:: infomark

7:08f69add4d06

  <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements">
    <requirement type="package" version="3.3.1">r</requirement>
  </expand>
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"
    
    #if str( $reference_source.reference_source_selector ) == "history":
        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
    #else:
        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if
    
    picard
    CollectBaseDistributionByCycle
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    CHART_OUTPUT="${pdfFile}"
    ALIGNED_READS_ONLY="${aligned_reads_only}"

    
    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR
  
  ]]></command>
  <inputs>
    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Load reference genome from">
        <option value="cached">Local cache</option>

      <param name="inputFile" value="picard_CollectBaseDistributionByCycle.bam" ftype="bam" />
      <output name="outFile" file="picard_CollectBaseDistributionByCycle_test1.tab" ftype="tabular" lines_diff="4"/>
    </test>
  </tests>
  
  
  <help>

.. class:: infomark