comparison repeatmasker.xml @ 5:19cc8c8f6f02 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 133126ca40437cebd8ead4ec14400dcc22b5ce21"

4:13b7842c72bc

<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy2" profile="17.01">
  <description>RepeatMasker</description>

  <requirements>
    <requirement type="package" version="4.0.7">repeatmasker</requirement>
  </requirements>

    ${advanced.xsmall}
    ${advanced.poly}
    rm_input.fasta &&
    #if $advanced.is_only != '-is_only':
      mv rm_input.fasta.masked '${output_masked_genome}' &&
      sed -r 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g ;  1,2c SW score\t% div.\t% del.\t% ins.\tquery sequence\tpos in  query: begin\tend\t(left)\trepeat\tclass/family\tpos in repeat: begin\tend\t(left)\tID' rm_input.fasta.out >'${output_log}' &&
      mv rm_input.fasta.tbl '${output_table}' &&
      #if $gff == '-gff':
        mv rm_input.fasta.out.gff '${output_gff}' &&
      #end if
      #if $advanced.keep_alignments == '-ali':
        mv rm_input.fasta.align '${output_alignment}' &&
      #end if
      #if $advanced.poly == '-poly':
        sed -r 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g' rm_input.fasta.polyout >'${output_polymorphic}' &&
      #end if
    #end if
    if [ -f 'rm_input.fasta.cat.gz' ]; then
      zcat 'rm_input.fasta.cat.gz' > '${output_repeat_catalog}';
    else

    <test expect_num_outputs="4">
      <param name="input_fasta" value="small.fasta" ftype="fasta" />
      <param name="source_type" value="library" />
      <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />
      <output name="output_masked_genome" file="small.fasta.masked" />
      <output name="output_table" file="small.fasta.stats" lines_diff="4" />
      <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
      <output name="output_log" file="small.fasta.log" />
    </test>
    <test expect_num_outputs="7">
      <param name="input_fasta" value="small.fasta" ftype="fasta" />

5:19cc8c8f6f02

<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy2" profile="17.01">
  <description>screen DNA sequences for interspersed repeats and low complexity regions</description>

  <requirements>
    <requirement type="package" version="4.0.7">repeatmasker</requirement>
  </requirements>

    ${advanced.xsmall}
    ${advanced.poly}
    rm_input.fasta &&
    #if $advanced.is_only != '-is_only':
      mv rm_input.fasta.masked '${output_masked_genome}' &&
      sed -E 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g ;  1,2c SW score\t% div.\t% del.\t% ins.\tquery sequence\tpos in  query: begin\tend\t(left)\trepeat\tclass/family\tpos in repeat: begin\tend\t(left)\tID' rm_input.fasta.out >'${output_log}' &&
      mv rm_input.fasta.tbl '${output_table}' &&
      #if $gff == '-gff':
        mv rm_input.fasta.out.gff '${output_gff}' &&
      #end if
      #if $advanced.keep_alignments == '-ali':
        mv rm_input.fasta.align '${output_alignment}' &&
      #end if
      #if $advanced.poly == '-poly':
        sed -E 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g' rm_input.fasta.polyout >'${output_polymorphic}' &&
      #end if
    #end if
    if [ -f 'rm_input.fasta.cat.gz' ]; then
      zcat 'rm_input.fasta.cat.gz' > '${output_repeat_catalog}';
    else

    <test expect_num_outputs="4">
      <param name="input_fasta" value="small.fasta" ftype="fasta" />
      <param name="source_type" value="library" />
      <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />
      <output name="output_masked_genome" file="small.fasta.masked" />
      <output name="output_table" file="small.fasta.stats" lines_diff="6" />
      <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
      <output name="output_log" file="small.fasta.log" />
    </test>
    <test expect_num_outputs="7">
      <param name="input_fasta" value="small.fasta" ftype="fasta" />