comparison summary.single.xml @ 8:88d39b1679df draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ff56a4c9218ddea84ff5cd72fd98c62db212465d"

7:72be09dfd803

<tool profile="16.07" id="mothur_summary_single" name="Summary.single" version="@WRAPPER_VERSION@.0">
    <description>Summary of calculator values for OTUs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
#if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode):
    && mv otu.*ave_std.summary otu.ave-std
#end if
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
        <param name="label" type="select" label="label - OTU Labels" multiple="true">

            <filter>otu.extension == 'mothur.shared' and not groupmode</filter>
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.summary" format="tabular"/>
        </collection>
    </outputs>
    <tests>
        <test><!-- test with shared and default params -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <output name="summary" md5="eaf5304b383c3c5764193ac7f49589db" ftype="tabular"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>

8:88d39b1679df

<tool profile="16.07" id="mothur_summary_single" name="Summary.single" version="@WRAPPER_VERSION@.2">
    <description>Summary of calculator values for OTUs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
#if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode):
    && mv otu.*ave[_-]std.summary otu.ave-std
#end if
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
        <param name="label" type="select" label="label - OTU Labels" multiple="true">

            <filter>otu.extension == 'mothur.shared' and not groupmode</filter>
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.summary" format="tabular"/>
        </collection>
    </outputs>
    <tests>
        <test><!-- test with shared and subsampling -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="use" value="yes"/>
            <output name="summary" md5="eaf5304b383c3c5764193ac7f49589db" ftype="tabular"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with shared and default params -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <output name="summary" md5="eaf5304b383c3c5764193ac7f49589db" ftype="tabular"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>