comparison picard_FilterSamReads.xml @ 7:08f69add4d06 draft

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

6:961236c5ec73

  <description>include or exclude aligned and unaligned reads and read lists</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>
    @java_options@
    
    ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order
    
    java -jar \$JAVA_JAR_PATH/picard.jar
    SortSam
    INPUT="${inputFile}"
    OUTPUT=query_sorted_bam.bam
    SORT_ORDER=queryname
    VALIDATION_STRINGENCY=LENIENT
    QUIET=true
    VERBOSITY=ERROR
    
    &amp;&amp;
    
    java -jar \$JAVA_JAR_PATH/picard.jar
    FilterSamReads
    INPUT=query_sorted_bam.bam
    FILTER="${filter_type.filter}"
    
    #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ):

    SORT_ORDER=coordinate
    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR
  
  </command>
  <inputs>
    <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
    <conditional name="filter_type">
      <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info">
        <option value="includeAligned">Include aligned</option>

    <test>
      <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
      <param name="filter" value="includeReadList"/>
      <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
      <param name="validation_stringency" value="LENIENT"/>
      <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="2"/>
    </test>
    <test>
      <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
      <param name="filter" value="excludeReadList"/>
      <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
      <param name="validation_stringency" value="LENIENT"/>
      <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="2"/>
    </test>
  </tests>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <help>

**Purpose**

7:08f69add4d06

  <description>include or exclude aligned and unaligned reads and read lists</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    
    ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order
    
    picard
    SortSam
    INPUT="${inputFile}"
    OUTPUT=query_sorted_bam.bam
    SORT_ORDER=queryname
    VALIDATION_STRINGENCY=LENIENT
    QUIET=true
    VERBOSITY=ERROR
    
    &&
    
    picard
    FilterSamReads
    INPUT=query_sorted_bam.bam
    FILTER="${filter_type.filter}"
    
    #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ):

    SORT_ORDER=coordinate
    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR
  
  ]]></command>
  <inputs>
    <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
    <conditional name="filter_type">
      <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info">
        <option value="includeAligned">Include aligned</option>

    <test>
      <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
      <param name="filter" value="includeReadList"/>
      <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
      <param name="validation_stringency" value="LENIENT"/>
      <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="4"/>
    </test>
    <test>
      <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
      <param name="filter" value="excludeReadList"/>
      <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
      <param name="validation_stringency" value="LENIENT"/>
      <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="4"/>
    </test>
  </tests>
  
  
  <help>

**Purpose**