view remove.dists.xml @ 1:0ec8be51451b draft

planemo upload for repository commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
author iuc
date Tue, 05 Sep 2017 17:03:44 -0400
parents 741303a463c8
children 0df1987fb914
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<tool profile="16.07" id="mothur_remove_dists" name="Remove.dists" version="@WRAPPER_VERSION@.0">
    <description>Removes distances from a phylip or column file</description>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>

        ## create symlinks to input datasets
        ln -s "$accnos" accnos.dat &&
        ln -s "$input.dist" input_dist.dat &&

        echo 'remove.dists(
            #if $input.source == "phylip":
            #end if
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
        <conditional name="input">
            <param name="source" type="select" label="Select input format">
                <option value="column">Pairwise Column Distance Matrix</option>
                <option value="phylip">Phylip Distance Matrix</option>
            <when value="column">
                <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
            <when value="phylip">
                <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
        <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/>
        <expand macro="logfile-output"/>
        <data name="pick_dist" format_source="dist" from_work_dir="input_dist*.pick.dat" label="${} on ${on_string}: pick.dist"/>
            <param name="source" value="phylip"/>
            <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
            <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/>
            <output name="pick_dist" md5="ec444ddb897d21864a245e8645fcda33" ftype="mothur.square.dist"/>
            <expand macro="logfile-test"/>


**Command Documentation**

The remove.dists_ removes distances from a phylip or column file related to groups or sequences listed in an accnos file.

.. _remove.dists:

    <expand macro="citations"/>