view read_counter.xml @ 0:cac6401377d2 draft default tip

planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty

<tool id="read_counter" name="readCounter" version="0.1.1">
  <description>
    Get Binned Read Distribution for a Sequence Alignment File
  </description>
  <requirements>
    <requirement type="package" version="0.1.1">hmmcopy</requirement>
  </requirements>
  <command>
    <![CDATA[
    
    ln -s $input_bam input.bam;
    ln -s $input_bam.metadata.bam_index input.bam.bai;
    
    #if $interval
    for i in \$( cat $interval ); do
    #end if
    
    readCounter 

    #if $interval
    -c \$i 
    #end if

    input.bam >> $output

    #if $interval
    ; done 
    #end if 

    ]]>
  </command>
  <inputs>
    <param type="data" format="bam" name="input_bam" label="Specify BAM Alignment File"/>
    <param type="data" format="bed,txt" name="interval" label="Specify Interval" optional="true"/>
  </inputs>
  <outputs>
    <data format="wig" name="output"/>
  </outputs>
</tool>