comparison trimmer.xml @ 2:a8fd651dcbd9 draft

"planemo upload commit 9a5d91c35d21411a0733cd233ca588ff358aabd8-dirty"

1:7ef568cbf13b

<?xml version="1.0"?>
<tool id="sequence_content_trimmer" version="0.2.1" name="Sequence Content Trimmer">
  <description>trim reads based on certain bases</description>
  <command detect_errors="exit_code"><![CDATA[
  #if $paired.is_paired and (('fasta' in $input1.extension and 'fastq' in $input2.extension) or \
      ('fastq' in $input1.extension and 'fasta' in $input2.extension))
    echo 'Both input files must be either fastq or fasta (no mixing the two).' >&2

    #elif $input1.extension == 'fasta'
      -f fasta
    #else
      -f $input1.extension
    #end if
    -b $bases -t $thres -w $win_len $invert
    #if $min_len.has_min_len:
      -m $min_len.value
    #end if
    #if not $paired.is_paired:
      > $output1

2:a8fd651dcbd9

<?xml version="1.0"?>
<tool id="sequence_content_trimmer" version="0.2.2" name="Sequence Content Trimmer">
  <description>trim reads based on certain bases</description>
  <command detect_errors="exit_code"><![CDATA[
  #if $paired.is_paired and (('fasta' in $input1.extension and 'fastq' in $input2.extension) or \
      ('fastq' in $input1.extension and 'fasta' in $input2.extension))
    echo 'Both input files must be either fastq or fasta (no mixing the two).' >&2

    #elif $input1.extension == 'fasta'
      -f fasta
    #else
      -f $input1.extension
    #end if
    -b '$bases' -t $thres -w $win_len $invert
    #if $min_len.has_min_len:
      -m $min_len.value
    #end if
    #if not $paired.is_paired:
      > $output1