comparison repeatmasker.xml @ 11:72aade318318 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit c4bf14b461856220df4b4bbdbb4b9bbad1ff8749"

10:bfc70c8cc5ca

<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.1.1" profile="17.01">
  <description>screen DNA sequences for interspersed repeats and low complexity regions</description>

  <requirements>
    <requirement type="package" version="4.1.1">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 &&
    #if $repeat_source.source_type == "dfam_up":

            <option value="yes" selected="true">Yes</option>
            <option value="no">No</option>
          </param>
          <when value="yes">
            <param name="species_list" type="select" label="Species">
              <option value="vertebrate">Vertebrate (other than below)</option>
              <option value="mammal">Mammal (other than below)</option>
              <option value="human" selected="true">Human</option>
              <option value="rodent">Rodent</option>
              <option value="mouse">Mouse</option>
              <option value="rat">Rat</option>
              <option value="danio">Danio (zebra fish)</option>
              <option value="drosophila">Fruit fly (Drosophila melanogaster)</option>
              <option value="elegans">Caenorhabditis elegans (nematode)</option>
            </param>
          </when>

      <output name="output_masked_genome" file="small_dfam_up.fasta.masked" />
      <output name="output_table" file="small_dfam_up.fasta.stats" lines_diff="2" />
      <output name="output_repeat_catalog" file="small_dfam_up.fasta.cat" lines_diff="2" />
      <output name="output_log" file="small_dfam_up.fasta.log" lines_diff="2"/>
    </test>
  </tests>
  <help><![CDATA[
RepeatMasker is a program that screens DNA for interspersed repeats and low
complexity DNA sequences. The database of repeats to screen for can be
provided as a FASTA file or downloaded from RepBase_. If the RepBase option is

.. _RepBase: http://www.girinst.org/repbase/
.. _homepage: http://www.repeatmasker.org/webrepeatmaskerhelp.html
    ]]>
  </help>
  <citations>
    <citation type="bibtex">
      @misc{RepeatMasker,
        title = {RepeatMasker Open-4.0},
        howpublished = {\url{http://www.repeatmasker.org}},
        author = {Smit, AFA and Hubley, R and Green, P.},
        year = {2013-2015}}
    </citation>
  </citations>
</tool>

11:72aade318318

<tool id="repeatmasker_wrapper" name="RepeatMasker" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">
    <description>screen DNA sequences for interspersed repeats and low complexity regions</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='xrefs'/>
    <expand macro='edam_ontology' />
    <expand macro='requirements' />
    <version_command>repeatmasker --version</version_command>
    <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 &&
    #if $repeat_source.source_type == "dfam_up":

            <option value="yes" selected="true">Yes</option>
            <option value="no">No</option>
          </param>
          <when value="yes">
            <param name="species_list" type="select" label="Species">
              <option value="human" selected="true">Human (Homo sapiens)</option>
              <option value="rodent">Rodent (Order Rodentia)</option>
              <option value="mouse">Mouse (Mus musculus)</option>
              <option value="rattus">Rat (Rattus sp.)</option>
              <option value="danio">Danio (zebra fish)</option>
              <option value="drosophila">Fruit fly (Drosophila melanogaster)</option>
              <option value="elegans">Caenorhabditis elegans (nematode)</option>
            </param>
          </when>

      <output name="output_masked_genome" file="small_dfam_up.fasta.masked" />
      <output name="output_table" file="small_dfam_up.fasta.stats" lines_diff="2" />
      <output name="output_repeat_catalog" file="small_dfam_up.fasta.cat" lines_diff="2" />
      <output name="output_log" file="small_dfam_up.fasta.log" lines_diff="2"/>
    </test>
    <test expect_num_outputs="4">
      <param name="input_fasta" value="small.fasta" ftype="fasta" />
      <param name="source_type" value="dfam" />
      <param name="species_list" value="rattus" />
      <output name="output_masked_genome" file="small_dfam_rattus.fasta.masked" />
      <output name="output_table" file="small_dfam_rattus.fasta.stats" lines_diff="2" />
      <output name="output_repeat_catalog" file="small_dfam_rattus.fasta.cat" lines_diff="2" />
      <output name="output_log" file="small_dfam_rattus.fasta.log" lines_diff="2"/>
    </test>
  </tests>
  <help><![CDATA[
RepeatMasker is a program that screens DNA for interspersed repeats and low
complexity DNA sequences. The database of repeats to screen for can be
provided as a FASTA file or downloaded from RepBase_. If the RepBase option is

.. _RepBase: http://www.girinst.org/repbase/
.. _homepage: http://www.repeatmasker.org/webrepeatmaskerhelp.html
    ]]>
  </help>
  <expand macro="citations" />
</tool>