annotate deunique.seqs.xml @ 3:77d86bdf1fa7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 283d5933cd945b7815b3da2ce45baa60d73e9746

<tool profile="16.07" id="mothur_deunique_seqs" name="Deunique.seqs" version="@WRAPPER_VERSION@.0">
    <description>Return all sequences</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 '$fasta' fasta.dat &&
ln -s '$names' names.dat &&

 echo 'deunique.seqs(
    #if $inputtype.intype == "countfile":
        count=names.dat,
    #else
        name=names.dat,
    #end if
    fasta=fasta.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
        <conditional name="inputtype">
            <param name="intype" type="select" label="type of file to provide, may be either a names or a count file" help="">
                <option value="namesfile">names</option>
                <option value="countfile">count table</option>
            </param>
            <when value="namesfile">
                <param name="names" type="data" format="mothur.names" label="provide a names file" help="A names file will generate a new faste file containing all the sequences."/>
            </when>
            <when value="countfile">
                <param name="names" type="data" format="mothur.count_table" label="provide a count table"
                    help="A counts table will generate a new faste file containing all the sequences.
                    If the file contains group information, a group file will also be created."/>
            </when>
        </conditional>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.redundant.fasta" label="${tool.name} on ${on_string}: fasta"/>
        <!-- groups file is created when a count file is used as input, but will be empty if the count file did not contain group information -->
        <data name="groups_file" format="mothur.groups" from_work_dir="names.redundant.groups" label="${tool.name} on ${on_string}: groups">
            <filter>inputtype.intype == 'countfile'</filter>
        </data>
    </outputs>
    <tests>
        <test><!-- test names file input -->
            <param name="fasta" value="amazon.unique.fasta"/>
            <param name="intype" value="namesfile"/>
            <param name="names" value="amazon.unique.names"/>
            <output name="out_fasta" md5="579698b8037ee939dd730e2cf0dd018d" ftype="fasta"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test count file input with group file output -->
            <param name="fasta" value="amazon.unique.fasta"/>
            <param name="intype" value="countfile"/>
            <param name="names" value="amazon_withgroups.count_table"/>
            <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
            <output name="groups_file" file="amazon_withgroups.redundant.groups" ftype="mothur.groups"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test count file input without group file output -->
            <param name="fasta" value="amazon.unique.fasta"/>
            <param name="intype" value="countfile"/>
            <param name="names" value="amazon.count_table"/>
            <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
            <output name="groups_file" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.groups"/> <!--empty-->
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The deunique.seqs_ command is the reverse of the unique.seqs command, and creates a fasta file from a fasta and name_ file.

.. _name: https://www.mothur.org/wiki/Name_file
.. _deunique.seqs: https://www.mothur.org/wiki/Deunique.seqs

v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output

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