comparison mitos.xml @ 4:c7553ba39670 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484

3:f20804c311de

<tool id="mitos" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
  <description>de-novo annotation of metazoan mitochondrial genomes</description>
  <xrefs>
      <xref type='bio.tools'>mitos</xref>
  </xrefs>
  <macros>
    <import>macros.xml</import>
    <token name="@MITOS_NAME@">MITOS</token>
    <token name="@TOOL_VERSION@">1.0.5</token>
    <token name="@VERSION_SUFFIX@">1</token>
  </macros>
  <requirements>
    <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
    <requirement type="package">zip</requirement>
  </requirements>
  <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
  <command detect_errors="aggressive"><![CDATA[
mkdir outdir &&

--clipfac $advanced_prot.clipfac
#set fragovl=float($advanced_prot.fragovl)/100.0
--fragovl $fragovl
--fragfac $advanced_prot.fragfac
--ststrange $advanced_prot.ststrange

#if "raw" in str($addoutputs).split(','):
  && zip -9 -y -r output.zip outdir/ > /dev/null
#end if
  ]]></command>
  <inputs>
    <param argument="--input" label="sequence" type="data" format="fasta" help="a single sequence in fasta formated sequence">
      <options options_filter_attribute="metadata.sequences">
        <filter type="add_value" value="1"/>
      </options>
    </param> 
    <param argument="--code" label="Genetic code" type="select">
      <option value="2">Vertebrate (2)</option>
      <option value="4">Mold, Protozoan, Coelenteral (4)</option>
      <option value="5">Invertebrate (5)</option>

      <filter>"protein_plot" in str(addoutputs)</filter>
    </data>
    <data name="ncRNA_plot_out" format="pdf" from_work_dir="outdir/plots/rna.pdf" label="${tool.name} on ${on_string}: ncRNA prediction plot">
      <filter>"protein_plot" in str(addoutputs)</filter>
    </data>
    <!--<collection name="ncRNA_structure_plot_ps_out" type="list" label="${tool.name} on ${on_string}: ncRNA postscript structure plots">
      <discover_datasets pattern="(?P&lt;name&gt;.+)\.ps" format="ps" directory="outdir/plots" />
      <filter>"ncRNA_structure_ps_plots" in str(addoutputs)</filter>
    </collection>-->
    <collection name="ncRNA_structure_plot_svg_out" type="list" label="${tool.name} on ${on_string}: ncRNA svg structure plots">
      <discover_datasets pattern="(?P&lt;name&gt;.+)\.svg" format="svg" directory="outdir/plots" />
      <filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter>
    </collection>
    <data name="rawout" format="zip" from_work_dir="output.zip" label="${tool.name} on ${on_string}: raw data">
      <filter>"raw" in str(addoutputs)</filter>
    </data>
  </outputs>
  <tests>
    <!-- default options -->

      <output name="seqout" file="NC_012920.seq" ftype="txt" />
      <output name="fasout" file="NC_012920.fas" ftype="fasta" />
      <output name="faaout" file="NC_012920.faa" ftype="fasta" />
      <output name="rawout" ftype="zip">
          <assert_contents>
              <has_archive_member path=".*/result.bed"/>
          </assert_contents>
      </output>
      <output name="geneorderout" file="NC_012920.geneorder" ftype="fasta" />
      <output name="protein_plot_out" file="NC_012920_prot.pdf" ftype="pdf" compare="sim_size"/>
      <output name="ncRNA_plot_out" file="NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/>

4:c7553ba39670

<tool id="mitos" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>de-novo annotation of metazoan mitochondrial genomes</description>
  <xrefs>
      <xref type='bio.tools'>mitos</xref>
  </xrefs>
  <macros>
    <import>macros.xml</import>
    <token name="@MITOS_NAME@">MITOS</token>
    <token name="@TOOL_VERSION@">1.1.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
  </macros>
  <requirements>
    <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
  </requirements>
  <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
  <command detect_errors="aggressive"><![CDATA[
mkdir outdir &&

--clipfac $advanced_prot.clipfac
#set fragovl=float($advanced_prot.fragovl)/100.0
--fragovl $fragovl
--fragfac $advanced_prot.fragfac
--ststrange $advanced_prot.ststrange
#if "raw" in str($addoutputs).split(','):
  --zip
#end if
  ]]></command>
  <inputs>
    <param argument="--input" label="sequence" type="data" format="fasta" help="a single sequence in fasta formated sequence">
      <validator type="dataset_metadata_in_range" metadata_name="sequences" min="1" max="1"/>
    </param> 
    <param argument="--code" label="Genetic code" type="select">
      <option value="2">Vertebrate (2)</option>
      <option value="4">Mold, Protozoan, Coelenteral (4)</option>
      <option value="5">Invertebrate (5)</option>

      <filter>"protein_plot" in str(addoutputs)</filter>
    </data>
    <data name="ncRNA_plot_out" format="pdf" from_work_dir="outdir/plots/rna.pdf" label="${tool.name} on ${on_string}: ncRNA prediction plot">
      <filter>"protein_plot" in str(addoutputs)</filter>
    </data>
    <collection name="ncRNA_structure_plot_svg_out" type="list" label="${tool.name} on ${on_string}: ncRNA svg structure plots">
      <discover_datasets pattern="(?P&lt;name&gt;.+)\.svg" format="svg" directory="outdir/plots" />
      <filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter>
    </collection>
    <data name="rawout" format="zip" from_work_dir="outdir.zip" label="${tool.name} on ${on_string}: raw data">
      <filter>"raw" in str(addoutputs)</filter>
    </data>
  </outputs>
  <tests>
    <!-- default options -->

      <output name="seqout" file="NC_012920.seq" ftype="txt" />
      <output name="fasout" file="NC_012920.fas" ftype="fasta" />
      <output name="faaout" file="NC_012920.faa" ftype="fasta" />
      <output name="rawout" ftype="zip">
          <assert_contents>
              <has_archive_member path="result.bed"/>
          </assert_contents>
      </output>
      <output name="geneorderout" file="NC_012920.geneorder" ftype="fasta" />
      <output name="protein_plot_out" file="NC_012920_prot.pdf" ftype="pdf" compare="sim_size"/>
      <output name="ncRNA_plot_out" file="NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/>