comparison picard_NormalizeFasta.xml @ 9:41b8d087a2d2 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f

8:e417b1d6288d

  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@

    ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
    ln -s '$inputFile' '$inputFile.element_identifier'.fa &&

    picard
    NormalizeFasta

    INPUT='$inputFile.element_identifier'.fa
    OUTPUT="${outFile}"
    LINE_LENGTH="${line_length}"
    TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"

    QUIET=true

9:41b8d087a2d2

  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@

    ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
    #import re
    #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
    ln -f -s '$inputFile' '$escaped_element_identifier'.fa &&
    picard
    NormalizeFasta

    INPUT='$escaped_element_identifier'.fa
    OUTPUT="${outFile}"
    LINE_LENGTH="${line_length}"
    TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"

    QUIET=true