comparison picard_CollectAlignmentSummaryMetrics.xml @ 10:777ccdd1d6e4 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

9:5eaa8a968300

<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.0">
  <description>writes a file containing summary alignment metrics</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <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
    CollectAlignmentSummaryMetrics
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    MAX_INSERT_SIZE=${maxinsert}
    #for $sequence in $adapters:
        ADAPTER_SEQUENCE="${sequence.adapter}"
    #end for
    METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
    IS_BISULFITE_SEQUENCED="${bisulphite}"
    
    REFERENCE_SEQUENCE="${reference_fasta_filename}"
    
    ASSUME_SORTED="${assume_sorted}"

    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR

    <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/>
    <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences">
          <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/>
    </repeat>
    <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/>
    
    <expand macro="VS" />
    
  </inputs>
  
  <outputs>
    <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
  </outputs>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  
  <tests>
    <test>
      <param name="bisulphite" value="false" />
      <param name="sorted" value="true" />
      <param name="adaptors" value="" />

      <param name="ref_file" value="picard_CASM_ref.fa" />
      <param name="inputFile" value="picard_CASM.bam" ftype="bam" />
      <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/>
    </test>
  </tests>
  
  <help>

.. class:: infomark

**Purpose**

10:777ccdd1d6e4

<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.1">
  <description>writes a file containing summary alignment metrics</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  <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
    CollectAlignmentSummaryMetrics
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    MAX_INSERT_SIZE=${maxinsert}
    #for $sequence in $adapters:
        ADAPTER_SEQUENCE="${sequence.adapter}"
    #end for
    #for $level in str($metric_accumulation_level).split(','):
        METRIC_ACCUMULATION_LEVEL="${level}"
    #end for
    IS_BISULFITE_SEQUENCED="${bisulphite}"

    REFERENCE_SEQUENCE="${reference_fasta_filename}"

    ASSUME_SORTED="${assume_sorted}"

    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR

    <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/>
    <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences">
          <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/>
    </repeat>
    <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/>
    <expand macro="VS" />

  </inputs>
  <outputs>
    <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
  </outputs>
  <tests>
    <test>
      <param name="bisulphite" value="false" />
      <param name="sorted" value="true" />
      <param name="adaptors" value="" />

      <param name="ref_file" value="picard_CASM_ref.fa" />
      <param name="inputFile" value="picard_CASM.bam" ftype="bam" />
      <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/>
    </test>
  </tests>
  <help>

.. class:: infomark

**Purpose**