comparison picard_EstimateLibraryComplexity.xml @ 7:08f69add4d06 draft

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

6:961236c5ec73

  <description>assess sequence library complexity from read sequences</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>
    @java_options@
    
    java -jar \$JAVA_JAR_PATH/picard.jar
    EstimateLibraryComplexity
    
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    

    
    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR
  
  </command>
  <inputs>
    <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
    <param name="min_identical_bases" type="integer" value="5" label="The minimum number of bases at the starts of reads that must be identical for reads to be grouped together for duplicate detection" help="MIN_IDENTICAL_BASES; In effect total_reads / 4^max_id_bases reads will be compared at a time, so lower numbers will produce more accurate results but consume exponentially more memory and CPU; default=5"/>
    <param name="max_diff_rate" type="float" value="0.03" label="The maximum rate of differences between two reads to call them identical" help="MAX_DIFF_RATE; default=0.03"/>
    <param name="min_mean_quality" type="integer" min="0" max="93" value="20" label="The minimum mean quality of the bases in a read pair for the read to be analyzed" help="MIN_MEAN_QUALITY; Reads with lower average quality are filtered out and not considered in any calculations; default=20"/>

      <param name="validation_stringency" value="LENIENT"/>
      <output name="outFile" file="picard_EstimateLibraryComplexity_test1.tab" ftype="tabular" lines_diff="4"/>
    </test>
  </tests>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <help>

**Purpose**

7:08f69add4d06

  <description>assess sequence library complexity from read sequences</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    
    picard
    EstimateLibraryComplexity
    
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    

    
    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR
  
  ]]></command>
  <inputs>
    <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
    <param name="min_identical_bases" type="integer" value="5" label="The minimum number of bases at the starts of reads that must be identical for reads to be grouped together for duplicate detection" help="MIN_IDENTICAL_BASES; In effect total_reads / 4^max_id_bases reads will be compared at a time, so lower numbers will produce more accurate results but consume exponentially more memory and CPU; default=5"/>
    <param name="max_diff_rate" type="float" value="0.03" label="The maximum rate of differences between two reads to call them identical" help="MAX_DIFF_RATE; default=0.03"/>
    <param name="min_mean_quality" type="integer" min="0" max="93" value="20" label="The minimum mean quality of the bases in a read pair for the read to be analyzed" help="MIN_MEAN_QUALITY; Reads with lower average quality are filtered out and not considered in any calculations; default=20"/>

      <param name="validation_stringency" value="LENIENT"/>
      <output name="outFile" file="picard_EstimateLibraryComplexity_test1.tab" ftype="tabular" lines_diff="4"/>
    </test>
  </tests>
  
  
  <help>

**Purpose**