annotate corr.axes.xml @ 10:b030bd08117b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab

<tool profile="16.07" id="mothur_corr_axes" name="Corr.axes" version="@WRAPPER_VERSION@.0">
    <description>correlation of data to axes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>

    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
#if $input.source == "shared":
    ln -s '$input.otu' input.otu.dat &&
#else
    ln -s '$input.metadata' input.metadata.dat &&
#end if

echo 'corr.axes(
    #if $input.source == "shared":
        #if $input.otu.is_of_type("mothur.relabund"):
            relabund=input.otu.dat,
        #elif $input.otu.is_of_type("mothur.shared"):
            shared=input.otu.dat,
        #end if
        #if $input.label:
            label=$input.label,
        #end if
        #if $input.groups:
            groups=${ str($input.groups).replace(",","-") },
        #end if
    #else:
        metadata=input.metadata.dat,
    #end if
    method=$method,
    axes=$axes,
    numaxes=$numaxes
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="axes" type="data" format="mothur.axes" label="axes - a pcoa axes dataset"/>
        <conditional name="input">
            <param name="source" type="select" label="Generate Collector Curvers for">
                <option value="shared">OTU Shared or Relabund</option>
                <option value="metadata">Metadata table</option>
            </param>
            <when value="shared">
                <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/>
                <param name="label" type="select" label="label - OTU Labels" multiple="false" optional="true">
                    <expand macro="labeloptions"/>
                </param>
                <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true">
                    <options>
                        <filter type="data_meta" ref="otu" key="groups"/>
                    </options>
                </param>
            </when>
            <when value="metadata">
                <param name="metadata" type="data" format="tabular" label="metadata - Table of floating point values"
                    help="metadata has the same number of rows as the samples, but the column(s) are floats that describe the samples (e.g. temperature, weight, etc.)"/>
            </when>
        </conditional>
        <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson">
                <option value="pearson" selected="true">pearson</option>
                <option value="spearman">spearman</option>
                <option value="kendall">kendall</option>
        </param>
        <param name="numaxes" type="integer" value="3" min="0" label="numaxes - Number of axes to use (default 3)"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="corr_axes" format="mothur.axes" from_work_dir="input.*.axes" label="${tool.name} on ${on_string}: corr.axes"/>
    </outputs>
    <tests>
        <test><!-- test with shared file -->
            <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/>
            <param name="source" value="shared"/>
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <output name="corr_axes" md5="34ff44b9a58780bc558afd1d22d96bb1" ftype="mothur.axes"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with metadata file -->
            <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/>
            <param name="source" value="metadata"/>
            <param name="metadata" value="amazon.metadata" ftype="tabular"/>
            <output name="corr_axes" md5="f62a3b7ed2b75312454a03ebbabe1edc" ftype="mothur.axes"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with relabund file and label and group select -->
            <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/>
            <param name="source" value="shared"/>
            <param name="label" value="0.05"/>
            <param name="groups" value="forest,pasture"/>
            <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
            <output name="corr_axes" md5="014f23f191ec6a9abbb82d51b3d5e24c" ftype="mothur.axes"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The corr.axes_ command calculates the correlation of data to axes.

.. _corr.axes: https://www.mothur.org/wiki/Corr.axes

v.1.21.0: Updated to mothur 1.33

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