comparison split.groups.xml @ 2:5f34cf40f36d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

1:addf3c859349

    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        @SHELL_OPTIONS@

        ## create symlinks to input datasets
        ln -s "$name" name.dat &&
        ln -s "$count" count.dat &&
        ln -s "$fasta" fasta.dat &&
        ln -s "$group" group.dat &&

        echo 'split.groups(
            #if $name:
                name=name.dat,
            #end if
            #if $groups:
                groups=${ str($groups).replace(",","-") },
            #end if
            #if $count:
                count=count.dat,
            #end if
            fasta=fasta.dat,
            group=group.dat
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/>
        <param name="name" type="data" format="mothur.names" label="name - Names to split by group" optional="true"/>
        <param name="group" type="data" format="mothur.groups" label="group - Groups"/>

            <options>
                <filter type="data_meta" ref="group" key="groups"/>
            </options>
        </param>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="groupfastas" type="list" label="${tool.name} on ${on_string}: fasta per group">
            <!-- TODO: format_source on discovered collection elements doesn't seem to work yet, change to format_source="fasta" once it does -->

            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
            <output_collection name="groupfastas" count="2">
                <element name="pasture" md5="3844bc02ec09acbbf31845ea6ac6632d" ftype="fasta"/>
                <element name="forest" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile.  A name_ file can also be split into groups.

.. _group: https://www.mothur.org/wiki/Group_file
.. _name: https://www.mothur.org/wiki/Name_file
.. _split.groups: https://www.mothur.org/wiki/Split.groups
]]>
    </help>
    <expand macro="citations"/>
</tool>

2:5f34cf40f36d

    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
ln -s '$name' name.dat &&
ln -s '$count' count.dat &&
ln -s '$fasta' fasta.dat &&
ln -s '$group' group.dat &&

echo 'split.groups(
    #if $name:
        name=name.dat,
    #end if
    #if $groups:
        groups=${ str($groups).replace(",","-") },
    #end if
    #if $count:
        count=count.dat,
    #end if
    fasta=fasta.dat,
    group=group.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/>
        <param name="name" type="data" format="mothur.names" label="name - Names to split by group" optional="true"/>
        <param name="group" type="data" format="mothur.groups" label="group - Groups"/>

            <options>
                <filter type="data_meta" ref="group" key="groups"/>
            </options>
        </param>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="groupfastas" type="list" label="${tool.name} on ${on_string}: fasta per group">
            <!-- TODO: format_source on discovered collection elements doesn't seem to work yet, change to format_source="fasta" once it does -->

            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
            <output_collection name="groupfastas" count="2">
                <element name="pasture" md5="3844bc02ec09acbbf31845ea6ac6632d" ftype="fasta"/>
                <element name="forest" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile.  A name_ file can also be split into groups.

.. _group: https://www.mothur.org/wiki/Group_file
.. _name: https://www.mothur.org/wiki/Name_file
.. _split.groups: https://www.mothur.org/wiki/Split.groups

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