annotate venn.xml @ 5:e4f4c1c0d193 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a

<tool profile="16.07" id="mothur_venn" name="Venn" version="@WRAPPER_VERSION@.0">
    <description>Generate Venn diagrams for groups </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 '$input.otu' input_otu.dat &&

echo 'venn(
    #if $input.source == "shared":
        shared=input_otu.dat,
        nseqs=$nseqs,
        permute=$permute,
        #if $input.groups:
            groups=${ str($input.groups).replace(",","-") },
        #end if
    #elif $input.source == "similarity":
        list=input_otu.dat,
        abund=$input.abund,
    #end if
    #if $input.label:
        label=${ str($input.label).replace(",","-") },
    #end if
    #if $input.calc:
        calc=${ str($input.calc).replace(",","-") },
    #end if
    fontsize=$fontsize,
    sharedotus=$sharedotus
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <conditional name="input">
            <param name="source" type="select" label="Generate Heatmap for">
                <option value="shared">OTU Shared</option>
                <option value="similarity">OTU list</option>
            </param>
            <when value="shared">
                <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
                <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
                    <option value="sharedsobs">Shared Sobs</option>
                    <option value="sharedchao">Shared Chao</option>
                    <option value="sharedace">Shared Ace</option>
                </param>
                <param name="label" type="select" multiple="true" label="label - OTU Labels">
                    <expand macro="labeloptions"/>
                </param>
                <param name="groups" type="select" multiple="true" label="groups - Groups to consider">
                    <options>
                        <filter type="data_meta" ref="otu" key="groups"/>
                    </options>
                </param>
            </when>
            <when value="similarity">
                <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
                <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
                    <option value="sobs">Sobs</option>
                    <option value="chao">Chao</option>
                    <option value="ace">Ace</option>
                </param>
                <param name="abund" type="integer" value="10" min="5" label="abund - Abundance when using the ace calculator ( >= 5 )"/>
                <param name="label" type="select" multiple="true" label="label - OTU Labels">
                    <expand macro="labeloptions"/>
                </param>
            </when>
        </conditional>
        <param name="nseqs" type="boolean" falsevalue="false" truevalue="true" checked="false" label="nseqs - Output the number of sequences represented by the otus in the picture"/>
        <param name="permute" type="select" label="permute - Create pictures with all possible 4-way permutations of groups">
            <option value="1">1</option>
            <option value="2">2</option>
            <option value="3">3</option>
            <option value="4" selected="true">4</option>
            <option value="true">true</option>
        </param>
        <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/>
        <param name="sharedotus" type="boolean" falsevalue="false" truevalue="true" checked="true" label="sharedotus - This parameter can be used with the sharedsobs calculator to get the names of the OTUs in each section of the venn diagram. Default=T"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <collection name="sharedotus_out" type="list" label="${tool.name} on ${on_string}: sharedotus">
            <filter>sharedotus</filter>
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.sharedotus" format="tabular"/>
        </collection>
        <collection name="svgs_out" type="list" label="${tool.name} on ${on_string}: svg">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.svg" format="svg"/>
        </collection>
        <expand macro="logfile-output"/>
    </outputs>
    <tests>
        <test><!-- test with shared file -->
            <param name="source" value="shared"/>
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="calc" value="sharedsobs,sharedchao"/>
            <param name="groups" value="forest,pasture"/>
            <output_collection name="sharedotus_out" count="35">
                <element name="0.05.sharedsobs.forest-pasture" md5="7513c9df64477a08b69f0d4665011e80" ftype="tabular" />
            </output_collection>
            <output_collection name="svgs_out" count="72">
                <element name="0.05.sharedsobs.forest-pasture" md5="e2dc0d5485520f5b22aa185ba91b123e" ftype="svg" />
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with list file -->
            <param name="source" value="similarity"/>
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="calc" value="sobs,chao,ace"/>
            <param name="groups" value="forest,pasture"/>
            <output_collection name="svgs_out" count="108">
                <element name=".0.45.ace" md5="d69778f507939bc2f5d2bbc3a0088f21" ftype="svg"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators

.. _venn: https://www.mothur.org/wiki/Venn

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