comparison mitos2.xml @ 7:b815ec682418 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit dfe519563a762fc72953e4754f76effe5e16cfec

6:af3c1dc1d141

  <description>de-novo annotation of metazoan mitochondrial genomes</description>
  <macros>
    <import>macros.xml</import>
    <token name="@MITOS_NAME@">MITOS2</token>
    <token name="@TOOL_VERSION@">2.1.7</token>
    <token name="@VERSION_SUFFIX@">0</token>
  </macros>
  <xrefs>
      <xref type="bio.tools">mitos</xref>
  </xrefs>
  <requirements>

--ncev $advanced_ncrna.ncev
$advanced_ncrna.sensitive
--maxtrnaovl $advanced_ncrna.maxtrnaovl
--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

        <has_text text="--maxrrnaovl 49"/>
        <not_has_text text="--noplots"/>
      </assert_command>
    </test>
    <!-- missing genes -->
    <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"/>

        <has_text text="--fragovl 0.2"/>
        <has_text text="--fragfac 10.0"/>
        <has_text text="--ncev 0.01"/>
        <has_text text="--maxtrnaovl 50"/>
        <has_text text="--maxrrnaovl 50"/>
        <has_text text="--noplots"/>
      </assert_command>
    </test>
  </tests>
  <help>@COMMON_HELP@
  <![CDATA[

7:b815ec682418

  <description>de-novo annotation of metazoan mitochondrial genomes</description>
  <macros>
    <import>macros.xml</import>
    <token name="@MITOS_NAME@">MITOS2</token>
    <token name="@TOOL_VERSION@">2.1.7</token>
    <token name="@VERSION_SUFFIX@">1</token>
  </macros>
  <xrefs>
      <xref type="bio.tools">mitos</xref>
  </xrefs>
  <requirements>

--ncev $advanced_ncrna.ncev
$advanced_ncrna.sensitive
--maxtrnaovl $advanced_ncrna.maxtrnaovl
--maxrrnaovl $advanced_ncrna.maxrrnaovl

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

        <has_text text="--maxrrnaovl 49"/>
        <not_has_text text="--noplots"/>
      </assert_command>
    </test>
    <!-- missing genes -->
    <test expect_num_outputs="3">
      <param name="input" value="NC_012920.fasta"/>
      <param name="code" value="2"/>
      <param name="refseqver" value="mitos2-refdata" />
      <param name="addoutputs" value="bed,missing,ncRNA_structure_svg_plots"/>
      <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>
      <output_collection name="ncRNA_structure_plot_svg_out" type="list" count="5"/>
      <assert_command>
        <has_text text="--code 2"/>
        <has_text text="--finovl 50"/>
        <not_has_text text="--trna"/>
        <not_has_text text="--rrna"/>

        <has_text text="--fragovl 0.2"/>
        <has_text text="--fragfac 10.0"/>
        <has_text text="--ncev 0.01"/>
        <has_text text="--maxtrnaovl 50"/>
        <has_text text="--maxrrnaovl 50"/>
        <has_text text="--noplots" negate="true"/>
      </assert_command>
    </test>
  </tests>
  <help>@COMMON_HELP@
  <![CDATA[