comparison metaquantome_db.xml @ 6:e63db1aa82ee draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761

5:860429737408

<tool id="metaquantome_db" name="metaQuantome: database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>download the GO, EC, and NCBI databases</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p data &&
        #set $database_list = str($databases).split(',')
        #for $d in $database_list
          metaquantome db '$d'
          --dir data &&
        #end for
        tar --create --file '$outfile' data
    ]]></command>
    <inputs>
        <param name="databases" type="select" multiple="True" display="checkboxes"
          label="Databases to Download">
          <option value="ncbi" selected="true">NCBI Taxonomy Database</option>
          <option value="go" selected="true">Gene Ontology Database</option>
          <option value="ec" selected="true">Enzyme Commission (EC) database</option>
        </param>
    </inputs>
    <outputs>
        <data format="tar" name="outfile" label="metaquantome databases"/>
    </outputs>
    <tests>
      <test>
        <param name="databases" value="go"/>
        <output name="outfile">
          <assert_contents>
            <has_text text="ontology: go"/>
            <has_text text="ontology: go/subsets/goslim_metagenomics"/>
          </assert_contents>
        </output>
      </test>
    </tests>
    <help>
<![CDATA[
metaQuantome database
=====================

Questions, Comments, Problems, Kudos
------------------------------------

Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
]]></help>
    <expand macro="citations" />
</tool>

6:e63db1aa82ee

<tool id="metaquantome_db" name="metaQuantome: database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>download the GO, EC, and NCBI databases</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p data &&
        #set $database_list = str($databases).split(',')
        #for $d in $database_list
          metaquantome db '$d'
          --dir data &&
        #end for
        tar --create --file '$outfile' data
    ]]></command>
    <inputs>
        <param name="databases" type="select" multiple="True" display="checkboxes" label="Databases to Download">
            <option value="ncbi" selected="true">NCBI Taxonomy Database</option>
            <option value="go" selected="true">Gene Ontology Database</option>
            <option value="ec" selected="true">Enzyme Commission (EC) database</option>
        </param>
    </inputs>
    <outputs>
        <data format="tar" name="outfile" label="metaquantome databases"/>
    </outputs>
    <tests>
        <test>
            <param name="databases" value="go"/>
            <output name="outfile">
                <assert_contents>
                    <has_text text="ontology: go"/>
                    <has_text text="ontology: go/subsets/goslim_metagenomics"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
metaQuantome database
=====================

Questions, Comments, Problems, Kudos
------------------------------------

Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
]]></help>
    <expand macro="citations"/>
</tool>