annotate get.coremicrobiome.xml @ 2:a1d38f9902d9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

<tool profile="16.07" id="mothur_get_coremicrobiome" name="Get.coremicrobiome" version="@WRAPPER_VERSION@.0">
    <description>fraction of OTUs for samples or abundances</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
ln -s '$otu' otu.dat &&

echo 'get.coremicrobiome(
    #if $otu.is_of_type("mothur.relabund"):
        relabund=otu.dat
    #elif $otu.is_of_type("mothur.shared"):
        shared=otu.dat
    #end if
    #if $label:
        ,label=${ str($label).replace(",","-") }
    #end if
    #if $groups:
        ,groups=${ str($groups).replace(",","-") }
    #end if
    #if $abundance:
        ,abundance=$abundance
    #end if
    #if $samples:
        ,samples=$samples
    #end if
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/>
        <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true">
            <expand macro="labeloptions"/>
        </param>
        <param name="groups" type="select" optional="true" label="groups - Pairwise comparision groups" multiple="true">
            <options>
                <filter type="data_meta" ref="otu" key="groups"/>
            </options>
        </param>
        <param name="abundance" type="integer" optional="true" value="" min="0" max="100" label="abundance - list OTU names at this abundance"/>
        <param name="samples" type="integer" optional="true" value="" min="1" label="samples - minimum number of samples requied to list OTU names"/>
        <param name="output" type="select" label="output - fraction or count">
            <option value="fraction" selected="true">fraction</option>
            <option value="count">count</option>
        </param>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="core_microbiome" type="list" label="${tool.name} on ${on_string}: core.microbiome files">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.core\.microbiome$" format="tabular"/>
        </collection>
        <collection name="core_microbiome_list" type="list" label="${tool.name} on ${on_string}: core.microbiome list files">
            <filter>abundance or samples </filter>
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.core\.microbiomelist" format="tabular"/>
        </collection>
    </outputs>
    <tests>
        <test><!-- test with default params -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <output_collection name="core_microbiome" count="36">
                <element name="0.45" md5="bae9cb5f1d311fe0cfb7ecb72a177261" ftype="tabular"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with list output and label and group select-->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="abundance" value="30"/>
            <param name="label" value="0.05,0.22,0.45"/>
            <param name="group" value="forest,pasture"/>
            <output_collection name="core_microbiome" count="3">
                <element name="0.05" md5="72bb437ab5f3a66965029a616fbaf317" ftype="tabular"/>
            </output_collection>
            <output_collection name="core_microbiome_list" count="3">
                <element name="0.05" md5="83722b4c52b7faff7fe56ce026250001" ftype="tabular"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The get.coremicrobiome_ command determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances.

.. _get.coremicrobiome: https://www.mothur.org/wiki/Get.coremicrobiome

v1.27.0: Updated to Mothur 1.33

    ]]></help>
    <expand macro="citations"/>
</tool>