comparison samtool_filter2.xml @ 13:aa8dc5cf70be draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit d02925461fc5d6188099a60c1996c671a0bde828

12:543405859e60

<tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.1">
  <description>files on FLAG MAPQ RG LN or by region</description>
  <requirements>
    <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command>

  ln -s "$input1.metadata.bam_index" input.bai &&
#elif isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sam').__class__):
  #set $input = 'input.sam'
  ln -s "$input1" $input &&
#end if
samtools view -o "$output1" $header

  #if $input1.datatype.file_ext == 'sam':
   -S
  #end if

    <param name="library" type="text" value="" label="Select alignments from Library"
           help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
    <param name="read_group" type="text" value="" label="Select alignments from Read Group"
           help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
    <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE" help="(-L)"/>
    <param name="regions" type="text" value="" label="Select regions (only used when the input is in BAM format)"
           help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/>
    <param name="outputtype" type="select" label="Select the output format">
        <option value="bam">BAM (-b)</option>
        <option value="sam">SAM</option>

13:aa8dc5cf70be

<tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.2">
  <description>files on FLAG MAPQ RG LN or by region</description>
  <requirements>
    <requirement type="package" version="1.2">samtools</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command>

  ln -s "$input1.metadata.bam_index" input.bai &&
#elif isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sam').__class__):
  #set $input = 'input.sam'
  ln -s "$input1" $input &&
#end if
samtools view $possibly_select_inverse "$output1" $header

  #if $input1.datatype.file_ext == 'sam':
   -S
  #end if

    <param name="library" type="text" value="" label="Select alignments from Library"
           help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
    <param name="read_group" type="text" value="" label="Select alignments from Read Group"
           help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
    <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE" help="(-L)"/>
    <param name="possibly_select_inverse" checked="false" label="Use inverse selection" type="boolean" truevalue="-U" falsevalue="-o" help="Select the opposite of the listed chromosomes" />
    <param name="regions" type="text" value="" label="Select regions (only used when the input is in BAM format)"
           help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/>
    <param name="outputtype" type="select" label="Select the output format">
        <option value="bam">BAM (-b)</option>
        <option value="sam">SAM</option>