comparison microsatbed.xml @ 4:25c70fff4079 draft default tip

planemo upload for repository https://github.com/fubar2/microsatbed commit d952bc313f408735456747c3d33e09a3170c8f59

3:36b8c6f7601b

<tool name="strtobed" id="microsatbedfubar" version="1.3.0" 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="1.3.0" type="package">pytrf</requirement>

      <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 $mode_cond.mode == "NATIVE":
    pytrf findstr -f '$mode_cond.outformat' -o $bed -r $mode_cond.monomin $mode_cond.dimin $mode_cond.trimin $mode_cond.tetramin $mode_cond.pentamin $mode_cond.hexamin '${reference_genome.fasta}' 
  #else:
    python '${__tool_directory__}/find_str.py'
    --fasta '${reference_genome.fasta}' 
    --bed '$bed'
    #if $mode_cond.mode == "SPECIFIC":
    --specific '$mode_cond.specific'
    --minreps '$mode_cond.minreps'
    #else:

]]></command>
  <inputs>
    <conditional name="reference_genome">
        <param name="genome_type_select" type="select" label="Select a source for fasta sequences to be searched for STRs" help="Options are to choose a built-in genome, or choose any history fasta file">
            <option value="indexed">Use a Galaxy server built-in reference genome fasta</option>
            <option selected="True" value="history">Use any fasta file from the current history</option>
        </param>
        <when value="indexed">
            <param name="fasta" type="select" optional="false" multiple="false" label="Choose a built-in, or custom reference genome" 
                help="If the genome you need is not on the list, add a custom genome or choose a genome fasta from the current history">
                <options from_data_table="all_fasta">
                    <filter column="2" type="sort_by"/>
                    <validator message="No genomes are available" type="no_options"/>
                </options>
            </param>
        </when>
        <when value="history">
            <param name="fasta" type="data" format="fasta,fasta.gz" optional="false" multiple="false" label="Choose a fasta file from the current history"/>
        </when>

        help="Short tandem repeats require 2 or more consecutive motifs by definition. WARNING: If monomers are included, every single matching base will be reported as a STR if minimum repeats = 1!"
        optional="false"/>
    </when>
    <when value="NATIVE">
      <param name="outformat" type="select" optional="false" label="Select the required output format" 
        help="Pytrf can create GFF, CSV or TSV output files">
        <option value="gff" selected="true">GFF</option>
        <option value="csv">Comma separated values</option>
        <option value="tsv">Tab separated values</option>
      </param>
      <param name="dimin" type="integer" value="2" min="1" label="Minimum number of repeats for dimers"/>
      <param name="trimin" type="integer" value="2" min="2" label="Minimum number of repeats for trimers"/>
      <param name="tetramin" type="integer" value="2" min="2" label="Minimum number of repeats for tetramers"/>
      <param name="pentamin" type="integer" value="2" min="2" label="Minimum number of repeats for pentamers"/>
      <param name="hexamin" type="integer" value="2" min="2" label="Minimum number of repeats for hexamers"/>
      <param name="monomin" type="integer" value="2" min="2" label="Minimum number of repeats for monomers"/>
    </when>
    </conditional>
  </inputs>
  <outputs>
    <data name="bed" format="bed" label="STR from $fasta.element_identifier" hidden="false">

4:25c70fff4079

<tool name="STR to bed" id="microsatbed" version="1.3.0" 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="1.3.0" type="package">pytrf</requirement>

      <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 $mode_cond.monomin $mode_cond.dimin $mode_cond.trimin $mode_cond.tetramin $mode_cond.pentamin $mode_cond.hexamin '${reference_genome.fasta}'
    #else:
      pytrf findstr -f '$mode_cond.outformat' -o $bed -r $mode_cond.monomin $mode_cond.dimin $mode_cond.trimin $mode_cond.tetramin $mode_cond.pentamin $mode_cond.hexamin '${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}'
    #else:
      --fasta '${reference_genome.fasta.fields.path}'
    #end if
    --bed '$bed'
    #if $mode_cond.mode == "SPECIFIC":
    --specific '$mode_cond.specific'
    --minreps '$mode_cond.minreps'
    #else:

]]></command>
  <inputs>
    <conditional name="reference_genome">
        <param name="genome_type_select" type="select" label="Select a source for fasta sequences to be searched for STRs" help="Options are to choose a built-in genome, or choose any history fasta file">
            <option value="indexed">Use a Galaxy server built-in reference genome fasta</option>
            <option value="history" selected="True">Use any fasta file from the current history</option>
        </param>
        <when value="indexed">
            <param name="fasta" type="select" multiple="false" label="Choose a built-in genome" 
                help="If the genome you need is not on the list, upload it and select it as a current history fasta">
                <options from_data_table="all_fasta"/>
            </param>
        </when>
        <when value="history">
            <param name="fasta" type="data" format="fasta,fasta.gz" optional="false" multiple="false" label="Choose a fasta file from the current history"/>
        </when>

        help="Short tandem repeats require 2 or more consecutive motifs by definition. WARNING: If monomers are included, every single matching base will be reported as a STR if minimum repeats = 1!"
        optional="false"/>
    </when>
    <when value="NATIVE">
      <param name="outformat" type="select" optional="false" label="Select the required output format" 
        help="Pytrf can create GFF, CSV or TSV output files. Documentation is linked in the help section below">
        <option value="gff" >GFF</option>
        <option value="csv">Comma separated values</option>
        <option value="tsv" selected="true">Tab separated values</option>
      </param>
      <param name="monomin" type="integer" value="2" min="2" label="Minimum number of repeats for monomers"/>
      <param name="dimin" type="integer" value="2" min="1" label="Minimum number of repeats for dimers"/>
      <param name="trimin" type="integer" value="2" min="2" label="Minimum number of repeats for trimers"/>
      <param name="tetramin" type="integer" value="2" min="2" label="Minimum number of repeats for tetramers"/>
      <param name="pentamin" type="integer" value="2" min="2" label="Minimum number of repeats for pentamers"/>
      <param name="hexamin" type="integer" value="2" min="2" label="Minimum number of repeats for hexamers"/>
    </when>
    </conditional>
  </inputs>
  <outputs>
    <data name="bed" format="bed" label="STR from $fasta.element_identifier" hidden="false">