view remove.otus.xml @ 0:4b07bc776ccb draft

planemo upload for repository commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:53:16 -0400
children 45d51905b3b5
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<tool profile="16.07" id="mothur_remove_otus" name="Remove.otus" version="@WRAPPER_VERSION@.0">
    <description>Remove otus containing sequences from specified groups</description>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>

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

        echo 'remove.otus(
            #if $groups:
                ,groups=${ str($groups).replace(",","-") }
            #end if
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
        <param name="label" type="select" label="label - OTU Labels" help="Select exactly one label">
            <expand macro="labeloptions"/>
        <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
        <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" help="At least one group must be selected">
                <filter type="data_meta" ref="group_in" key="groups"/>
        <expand macro="logfile-output"/>
        <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.dat" label="${} on ${on_string}: pick.groups"/>
        <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.dat" label="${} on ${on_string}: pick.list"/>
            <param name="otu" value="" ftype="mothur.list"/>
            <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
            <param name="groups" value="forest"/>
            <param name="label" value="0.05"/>
            <output name="list_out" md5="fa5b954ad8e8235dbb700af1a9d8a091" ftype="mothur.list"/>
            <output name="group_out" md5="3c9f6e88de0f60f2a870c8d4a9d61db8" ftype="mothur.groups"/>
            <expand macro="logfile-test"/>


**Command Documentation**

The remove.otus_ command removes otus from a list_ containing sequences from a specific group or set of groups.

.. _list:
.. _remove.otus:

    <expand macro="citations"/>