comparison picard_MergeBamAlignment.xml @ 12:05087b27692a draft

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

11:efc56ee1ade4

  <description>merge alignment data with additional info stored in an unmapped BAM dataset</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>
    @java_options@
    #set $picard_dict = "localref.dict"
    #set $ref_fasta = "localref.fa"     ## This is done because picards "likes" .fa extension
    
    ln -s "${reference_source.ref_file}" "${ref_fasta}" &amp;&amp;
       
    #if str( $reference_source.reference_source_selector ) == "history":
        
      java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
      QUIET=true
      VERBOSITY=ERROR
      
      &amp;&amp;
      
    #else:
    
      #set $ref_fasta = str( $reference_source.ref_file.fields.path )
    
    #end if
    
    java -jar \$JAVA_JAR_PATH/picard.jar
    MergeBamAlignment
      UNMAPPED_BAM="${unmapped_bam}"
      
      PAIRED_RUN=true ##This argument is ignored and will be removed. Required. Possible values: {true, false}
      

      SORT_ORDER=coordinate
      QUIET=true
      VERBOSITY=ERROR
      
  </command>
  
  <inputs>
    
     <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Load reference genome from">

      <param name="aligner_proper_pair_flags" value="False"/>
      <param name="primary_alignment_strategy" value="BestMapq"/>
      <param name="clip_overlapping_reads" value="True"/>
      <param name="include_secondary_alignments" value="True"/>
      <param name="add_mate_cigar" value="True"/>
      <output name="outFile" file="picard_MergeBamAlignment_test1.bam" ftype="bam" lines_diff="2"/>
    </test>
  </tests>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <help>

.. class:: infomark

12:05087b27692a

  <description>merge alignment data with additional info stored in an unmapped BAM dataset</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    #set $picard_dict = "localref.dict"
    #set $ref_fasta = "localref.fa"     ## This is done because picards "likes" .fa extension
    
    ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
       
    #if str( $reference_source.reference_source_selector ) == "history":
        
      picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
      QUIET=true
      VERBOSITY=ERROR
      
      &&
      
    #else:
    
      #set $ref_fasta = str( $reference_source.ref_file.fields.path )
    
    #end if
    
    picard
    MergeBamAlignment
      UNMAPPED_BAM="${unmapped_bam}"
      
      PAIRED_RUN=true ##This argument is ignored and will be removed. Required. Possible values: {true, false}
      

      SORT_ORDER=coordinate
      QUIET=true
      VERBOSITY=ERROR
      
  ]]></command>
  
  <inputs>
    
     <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Load reference genome from">

      <param name="aligner_proper_pair_flags" value="False"/>
      <param name="primary_alignment_strategy" value="BestMapq"/>
      <param name="clip_overlapping_reads" value="True"/>
      <param name="include_secondary_alignments" value="True"/>
      <param name="add_mate_cigar" value="True"/>
      <output name="outFile" file="picard_MergeBamAlignment_test1.bam" ftype="bam" lines_diff="4"/>
    </test>
  </tests>
  
  
  <help>

.. class:: infomark