comparison microsatbed.xml @ 30:53c4f91c6031 draft default tip

planemo upload for repository https://github.com/fubar2/microsatbed commit 80a8c0db54b6e2cab9dfe7178b1e5b3b39592f2c

29:efc775ab30fe

<tool name="STR to bed" id="microsatbed" version="1.3.2" profile="22.05">
  <description>Short Tandem Repeats to bed features from fasta</description>
  <requirements>
    <requirement version="3.12.3" type="package">python</requirement>
    <requirement version="2.1.0" type="package">pyfastx</requirement>
    <requirement version="1.3.2" type="package">pytrf</requirement>
    <requirement version="455" type="package">ucsc-bedgraphtobigwig</requirement>
     
  </requirements>
   <required_files>
      <include path="find_str.py"/>
  </required_files>
   <version_command><![CDATA[python -c "import pytrf; from importlib.metadata import version; print(version('pytrf'))"]]></version_command>
  <command><![CDATA[
  #if $mode_cond.mode == "NATIVE":
    #if $reference_genome.genome_type_select == "history":
      pytrf findstr -f '$mode_cond.outformat' -o $bed -r $monomin $dimin $trimin $tetramin $pentamin $hexamin '${reference_genome.fasta}'
    #else:
      pytrf findstr -f '$mode_cond.outformat' -o $bed -r $monomin $dimin $trimin $tetramin $pentamin $hexamin '${reference_genome.fasta.fields.path}'
    #end if
  #else:
    python '${__tool_directory__}/find_str.py'
    #if $reference_genome.genome_type_select == "history":
      --fasta '${reference_genome.fasta}'

        <option value="csv">Comma separated values</option>
        <option value="tsv" selected="true">Tab separated values</option>
      </param>
    </when>
    </conditional>
    <param type="integer" min="2" name="monomin" value="10"/>
    <param type="integer" min="1" name="dimin" value="3"/>
    <param type="integer" min="2" name="trimin" value="2"/>
    <param type="integer" min="2" name="tetramin" value="2"/>
    <param type="integer" min="2" name="pentamin" value="2"/>
    <param type="integer" min="2" name="hexamin" value="2"/>
  </inputs>
  <outputs>
    <data name="bed" format="bed" label="STR from $fasta.element_identifier" hidden="false">
      <change_format>
            <when input="mode_cond.outformat" value="gff" format="gff" />

30:53c4f91c6031

<tool name="STR to bed" id="microsatbed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
  <description>Short Tandem Repeats to bed features from fasta</description>
  <macros>
  <token name="@TOOL_VERSION@">1.3.2</token>
  <token name="@VERSION_SUFFIX@">0</token>
  <token name="@PYFASTX_VERSION@">2.1.0</token>
  <token name="@PYTHON_VERSION@">3.12.3</token>
  <token name="@UCSC_VERSION@">455</token>
  </macros>
  <requirements>
    <requirement version="@PYTHON_VERSION@" type="package">python</requirement>
    <requirement version="@PYFASTX_VERSION@" type="package">pyfastx</requirement>
    <requirement version="@TOOL_VERSION@" type="package">pytrf</requirement>
    <requirement version="@UCSC_VERSION@" type="package">ucsc-bedgraphtobigwig</requirement>
     
  </requirements>
   <required_files>
      <include path="find_str.py"/>
  </required_files>
   <version_command><![CDATA[python -c "import pytrf; from importlib.metadata import version; print(version('pytrf'))"]]></version_command>
  <command><![CDATA[
  #if $mode_cond.mode == "NATIVE":
    #if $reference_genome.genome_type_select == "history":
      pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.fasta}'
    #else:
      pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.fasta.fields.path}'
    #end if
  #else:
    python '${__tool_directory__}/find_str.py'
    #if $reference_genome.genome_type_select == "history":
      --fasta '${reference_genome.fasta}'

        <option value="csv">Comma separated values</option>
        <option value="tsv" selected="true">Tab separated values</option>
      </param>
    </when>
    </conditional>
    <param type="integer" label="Minimum repeats required for monomers" min="2" name="monomin" value="10"/>
    <param type="integer" label="Minimum repeats required for dimers" min="1" name="dimin" value="3"/>
    <param type="integer" label="Minimum repeats required for trimers" min="2" name="trimin" value="2"/>
    <param type="integer" label="Minimum repeats required for tetramers" min="2" name="tetramin" value="2"/>
    <param type="integer" label="Minimum repeats required for pentamers" min="2" name="pentamin" value="2"/>
    <param type="integer" label="Minimum repeats required for hexamers" min="2" name="hexamin" value="2"/>
  </inputs>
  <outputs>
    <data name="bed" format="bed" label="STR from $fasta.element_identifier" hidden="false">
      <change_format>
            <when input="mode_cond.outformat" value="gff" format="gff" />