annotate list.seqs.xml @ 0:24044cd8ef87 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d

<tool profile="16.07" id="mothur_list_seqs" name="List.seqs" version="@WRAPPER_VERSION@.0">
    <description>Lists the names (accnos) of the 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 "$search.input" search.input.dat &&

        echo 'list.seqs(
            #if $search.intype == "fasta":
                fasta=search.input.dat
            #elif $search.intype == "fastq":
                fastq=search.input.dat
            #elif $search.intype == "name":
                name=search.input.dat
            #else if $search.intype == "group":
                group=search.input.dat
            #elif $search.intype == "alignreport":
                alignreport=search.input.dat
            #elif $search.intype == "list":
                list=search.input.dat
            #elif $search.intype == "taxonomy":
                taxonomy=search.input.dat
            #elif $search.intype == "count":
                count=search.input.dat
            #end if
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <conditional name="search">
            <param name="intype" type="select" label="Type to list" help="">
                <option value="fasta">Sequence Fasta</option>
                <option value="fastq">Sequence Fastq</option>
                <option value="name">Sequences Name reference</option>
                <option value="group">Groups</option>
                <option value="alignreport">Align Report</option>
                <option value="list">OTU List</option>
                <option value="taxonomy">Sequence Taxonomy</option>
                <option value="count">Count Table</option>
            </param>
            <when value="fasta">
                <param name="input" type="data" format="fasta" label="fasta - Fasta"/>
            </when>
            <when value="fastq">
                <param name="input" type="data" format="fastq" label="fasta - Fasta"/>
            </when>
            <when value="name">
                <param name="input" type="data" format="mothur.names" label="name - Names"/>
            </when>
            <when value="group">
                <param name="input" type="data" format="mothur.groups" label="group - Groups"/>
            </when>
            <when value="alignreport">
                <param name="input" type="data" format="mothur.align.report" label="alignreport - Align Report"/>
            </when>
            <when value="list">
                <param name="input" type="data" format="mothur.list" label="list - OTU List"/>
            </when>
            <when value="taxonomy">
                <param name="input" type="data" format="mothur.seq.taxonomy" label="taxonomy - Sequence Taxonomy"/>
            </when>
            <when value="count">
                <param name="input" type="data" format="mothur.count_table" label="count - Count Table"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_file" format="mothur.accnos" from_work_dir="search.input*.accnos" label="${tool.name} on ${on_string}: accnos"/>
    </outputs>
    <tests>
        <test><!-- test with fasta -->
            <param name="intype" value="fasta"/>
            <param name="input" value="amazon.fasta"/>
            <output name="out_file" md5="590f62ce757219c2e137a532fcd814d1" ftype="mothur.accnos"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with count file -->
            <param name="intype" value="count"/>
            <param name="input" value="amazon.count_table"/>
            <output name="out_file" md5="360dfea2de2da4d55e75071b026c83b6" ftype="mothur.accnos"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The list.seqs_ command writes out the names of the sequences found within a fasta, name_, group_, list_, align.report_ or taxonomy_ file.

.. _name: https://www.mothur.org/wiki/Name_file
.. _group: https://www.mothur.org/wiki/Group_file
.. _list: https://www.mothur.org/wiki/List_file
.. _align.report: https://www.mothur.org/wiki/Align.seqs
.. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
.. _list.seqs: https://www.mothur.org/wiki/list.seqs

v.1.20.0: Updated to mothur 1.33, added count and fastq option
]]>
    </help>
    <expand macro="citations"/>
</tool>