comparison mitos2.xml @ 4:033755194fe9 draft

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

3:624606f7c996

<tool id="mitos2" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
  <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@">MITOS2</token>
    <token name="@TOOL_VERSION@">2.0.6</token>
    <token name="@VERSION_SUFFIX@">2</token>
  </macros>
  <requirements>
    <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
    <requirement type="package" version="3.0">zip</requirement>
  </requirements>
  <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
  <command detect_errors="aggressive"><![CDATA[
mkdir outdir &&

--maxrrnaovl $advanced_ncrna.maxrrnaovl

#if not ("protein_plot" in $addoutputs or "ncRNA_plot" in $addoutputs):
  --noplots
#end if

#if "missing" in $addoutputs:
    > outdir/missing.txt
#end if

#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 ${on_string}: ncRNA prediction plot">
      <filter>"ncRNA_plot" in str(addoutputs)</filter>
    </data>
    <!--<collection name="ncRNA_structure_plot_ps_out" type="list" label="${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 ${on_string}: raw data">
      <filter>"raw" in str(addoutputs)</filter>
    </data>
    <data name="missing_genes" format="txt" from_work_dir="outdir/missing.txt" label="${tool.name} on ${on_string}: missing genes">
      <filter>"missing" in str(addoutputs)</filter>
    </data>

    <!-- default options -->
    <test expect_num_outputs="1">
      <param name="input" value="NC_012920.fasta"/>
      <param name="code" value="2"/>
      <param name="refseqver" value="mitos2-refdata" />
      <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed"/>
      <assert_command>
        <has_text text="--code 2"/>
        <has_text text="--finovl 50"/>
        <not_has_text text="--trna"/>
        <not_has_text text="--rrna"/>

    <!-- different main options  -->
    <test expect_num_outputs="1">
      <param name="input" value="NC_012920.fasta"/>
      <param name="code" value="5"/>
      <param name="refseqver" value="mitos2-refdata" />
      <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed" compare="sim_size"/>
      <section name="advanced">
        <param name="featuretypes" value="prot,trna,rrna,intron,oril,orih"/>
        <param name="finovl" value="49"/>
        <param name="best" value="true"/>
        <param name="fragovl" value="10"/>

        <param name="sensitive" value="true"/>
        <param name="maxtrnaovl" value="51"/>
        <param name="maxrrnaovl" value="49"/>
      </section>
      <param name="addoutputs" value="bed,mito,gff,seq,fas,faa,geneorder,protein_plot,ncRNA_plot,ncRNA_structure_svg_plots,raw"/>
      <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed" compare="sim_size"/>
      <output name="mitoout" file="mitos2_NC_012920.mitos" ftype="tabular"/>
      <output name="gffout" file="mitos2_NC_012920.gff" ftype="gff"/>
      <output name="seqout" file="mitos2_NC_012920.seq" ftype="txt"/>
      <output name="faa" file="mitos2_NC_012920.faa" ftype="fasta"/>
      <output name="fas" file="mitos2_NC_012920.fas" ftype="fasta"/>
      <output name="geneorderout" file="mitos2_NC_012920.geneorder" ftype="fasta"/>
      <output name="protein_plot_out" file="mitos2_NC_012920_prot.pdf" ftype="pdf" compare="sim_size"/>
      <output name="ncRNA_plot_out" file="mitos2_NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/>
      <output name="rawout" ftype="zip">
        <assert_contents>
          <has_archive_member path=".*/result.bed"/>
        </assert_contents>
      </output>
      <output_collection name="ncRNA_structure_plot_svg_out" type="list" count="17"/>
      <assert_command>
        <has_text text="--code 2"/>

    <test expect_num_outputs="2">
      <param name="input" value="NC_012920.fasta"/>
      <param name="code" value="2"/>
      <param name="refseqver" value="mitos2-refdata" />
      <param name="addoutputs" value="bed,missing"/>
      <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed"/>
      <output name="missing_genes" file="missing_genes.txt" ftype="txt"/>
      <assert_command>
        <has_text text="--code 2"/>
        <has_text text="--finovl 50"/>
        <not_has_text text="--trna"/>
        <not_has_text text="--rrna"/>

4:033755194fe9

<tool id="mitos2" 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@">MITOS2</token>
    <token name="@TOOL_VERSION@">2.1.3</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 &&

--maxrrnaovl $advanced_ncrna.maxrrnaovl

#if not ("protein_plot" in $addoutputs or "ncRNA_plot" in $addoutputs):
  --noplots
#end if
#if "raw" in str($addoutputs).split(','):
  --zip
#end if

#if "missing" in $addoutputs:
    > outdir/missing.txt
#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 ${on_string}: ncRNA prediction plot">
      <filter>"ncRNA_plot" in str(addoutputs)</filter>
    </data>
    <collection name="ncRNA_structure_plot_svg_out" type="list" label="${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 ${on_string}: raw data">
      <filter>"raw" in str(addoutputs)</filter>
    </data>
    <data name="missing_genes" format="txt" from_work_dir="outdir/missing.txt" label="${tool.name} on ${on_string}: missing genes">
      <filter>"missing" in str(addoutputs)</filter>
    </data>

    <!-- default options -->
    <test expect_num_outputs="1">
      <param name="input" value="NC_012920.fasta"/>
      <param name="code" value="2"/>
      <param name="refseqver" value="mitos2-refdata" />
      <output name="bedout" file="mitos2_NC_012920.bed" compare="re_match" ftype="bed"/>
      <assert_command>
        <has_text text="--code 2"/>
        <has_text text="--finovl 50"/>
        <not_has_text text="--trna"/>
        <not_has_text text="--rrna"/>

    <!-- different main options  -->
    <test expect_num_outputs="1">
      <param name="input" value="NC_012920.fasta"/>
      <param name="code" value="5"/>
      <param name="refseqver" value="mitos2-refdata" />
      <output name="bedout" ftype="bed">
        <assert_contents>
          <has_n_lines n="8"/>
        </assert_contents>
      </output>
      <section name="advanced">
        <param name="featuretypes" value="prot,trna,rrna,intron,oril,orih"/>
        <param name="finovl" value="49"/>
        <param name="best" value="true"/>
        <param name="fragovl" value="10"/>

        <param name="sensitive" value="true"/>
        <param name="maxtrnaovl" value="51"/>
        <param name="maxrrnaovl" value="49"/>
      </section>
      <param name="addoutputs" value="bed,mito,gff,seq,fas,faa,geneorder,protein_plot,ncRNA_plot,ncRNA_structure_svg_plots,raw"/>
      <output name="bedout" ftype="bed">
        <assert_contents>
          <has_n_lines n="18"/>
        </assert_contents>
      </output>
      <output name="mitoout" file="mitos2_NC_012920.mitos" compare="re_match" ftype="tabular"/>
      <output name="gffout" file="mitos2_NC_012920.gff" compare="re_match" ftype="gff"/>
      <output name="seqout" file="mitos2_NC_012920.seq" ftype="txt"/>
      <output name="faa" file="mitos2_NC_012920.faa" ftype="fasta"/>
      <output name="fas" file="mitos2_NC_012920.fas" ftype="fasta"/>
      <output name="geneorderout" file="mitos2_NC_012920.geneorder" ftype="fasta"/>
      <output name="protein_plot_out" file="mitos2_NC_012920_prot.pdf" ftype="pdf" compare="sim_size"/>
      <output name="ncRNA_plot_out" file="mitos2_NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/>
      <output name="rawout" ftype="zip">
        <assert_contents>
          <has_archive_member path="result.bed"/>
        </assert_contents>
      </output>
      <output_collection name="ncRNA_structure_plot_svg_out" type="list" count="17"/>
      <assert_command>
        <has_text text="--code 2"/>

    <test expect_num_outputs="2">
      <param name="input" value="NC_012920.fasta"/>
      <param name="code" value="2"/>
      <param name="refseqver" value="mitos2-refdata" />
      <param name="addoutputs" value="bed,missing"/>
      <output name="bedout" file="mitos2_NC_012920.bed" compare="re_match" ftype="bed"/>
      <output name="missing_genes" ftype="txt">
        <assert_contents>
          <has_size value="167"/>
        </assert_contents>
      </output>
      <assert_command>
        <has_text text="--code 2"/>
        <has_text text="--finovl 50"/>
        <not_has_text text="--trna"/>
        <not_has_text text="--rrna"/>