comparison repeatmasker.xml @ 6:65ab76d58c41 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 6cf009024dfff81b0e0f836b76cf475e7cf84c71

5:8404aa79a631

<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy1" profile="17.01">
  <description>RepeatMasker</description>

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

  <command detect_errors="exit_code"><![CDATA[
    RM_LIB_PATH=\$(dirname \$(which RepeatMasker))/../share/RepeatMasker/Libraries &&
    mkdir lib &&
    export REPEATMASKER_LIB_DIR=\$(pwd)/lib &&
      for file in \$(ls \$RM_LIB_PATH) ; do  ln -s \$RM_LIB_PATH/\$file lib/\$file ; done &&
    #if $repeat_source.source_type == "repbase":
      cp '${repeat_source.repbase_file}' 'lib/${repeat_source.repbase_file_name}' &&

    <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="2" />
      <output name="output_repeat_catalog" file="small.fasta.cat" />
      <output name="output_log" file="small.fasta.log" />
    </test>
    <test expect_num_outputs="7">
      <param name="input_fasta" value="small.fasta" ftype="fasta" />
      <param name="source_type" value="library" />

      <!-- <param name="show" value="yes" /> -->
      <param name="keep_alignments" value="-ali" />
      <param name="poly" value="-poly" />
      <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" />
      <output name="output_log" file="small.fasta.log" />
      <output name="output_alignment" file="small.fasta.align" />
      <output name="output_polymorphic" file="small.fasta.poly" />
      <output name="output_gff" file="small.fasta.gff" lines_diff="4" />
    </test>

      <param name="repbase_file" value="fake_repbase.embl" />
      <param name="repbase_file_name" value="fake.embl" />
      <param name="species_list" value="anopheles" />
      <output name="output_masked_genome" file="small.fasta.masked" />
      <output name="output_table" file="small_repbase.fasta.stats" lines_diff="2" />
      <output name="output_repeat_catalog" file="small.fasta.cat" />
      <output name="output_log" file="small_repbase.fasta.log" />
    </test>
  </tests>
  <help><![CDATA[
RepeatMasker is a program that screens DNA for interspersed repeats and low

6:65ab76d58c41

<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>

  <command detect_errors="exit_code"><![CDATA[
    RM_PATH=\$(which RepeatMasker) && 
    if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&
    RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries &&
    mkdir lib &&
    export REPEATMASKER_LIB_DIR=\$(pwd)/lib &&
      for file in \$(ls \$RM_LIB_PATH) ; do  ln -s \$RM_LIB_PATH/\$file lib/\$file ; done &&
    #if $repeat_source.source_type == "repbase":
      cp '${repeat_source.repbase_file}' 'lib/${repeat_source.repbase_file_name}' &&

    <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" />
      <param name="source_type" value="library" />

      <!-- <param name="show" value="yes" /> -->
      <param name="keep_alignments" value="-ali" />
      <param name="poly" value="-poly" />
      <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" />
      <output name="output_alignment" file="small.fasta.align" />
      <output name="output_polymorphic" file="small.fasta.poly" />
      <output name="output_gff" file="small.fasta.gff" lines_diff="4" />
    </test>

      <param name="repbase_file" value="fake_repbase.embl" />
      <param name="repbase_file_name" value="fake.embl" />
      <param name="species_list" value="anopheles" />
      <output name="output_masked_genome" file="small.fasta.masked" />
      <output name="output_table" file="small_repbase.fasta.stats" lines_diff="2" />
      <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
      <output name="output_log" file="small_repbase.fasta.log" />
    </test>
  </tests>
  <help><![CDATA[
RepeatMasker is a program that screens DNA for interspersed repeats and low