comparison picard_CollectAlignmentSummaryMetrics.xml @ 27:fdca9493e09b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 70d2a66c405be58d4413753792bcadf212a4da84

26:fc3866ddc7b6

<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>writes a file containing summary alignment metrics</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">1</token>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@

    <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="maxinsert" value="100000" />
      <param name="reference_source_selector" value="history" />
      <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"/>

27:fdca9493e09b

<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>writes a file containing summary alignment metrics</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">2</token>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@

    <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}: tablular"/>
  </outputs>
  <tests>
    <test>
      <param name="bisulphite" value="false" />
      <param name="assume_sorted" value="true" />
      <repeat name="adapters">
        <param name="adapter" value = ""/>
      </repeat>
      <param name="maxinsert" value="100000" />
      <param name="reference_source_selector" value="history" />
      <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"/>