<tool profile="16.07" id="mothur_remove_groups" name="Remove.groups" version="@WRAPPER_VERSION@.0">
    <description>Remove groups from groups,fasta,names,list,taxonomy</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
#if $groupnames.source == "other":
    ln -s '$groupnames.group_in' groupnames_group_in.dat &&
    ln -s '$groupnames.fasta_in' groupnames_fasta_in.dat &&
    ln -s '$groupnames.name_in' groupnames_name_in.dat &&
    ln -s '$groupnames.list_in' groupnames_list_in.dat &&
    ln -s '$groupnames.taxonomy_in' groupnames_taxonomy_in.dat &&
    ln -s '$groupnames.column_in' groupnames_column_in.dat &&
    ln -s '$groupnames.phylip_in' groupnames_phylip_in.dat &&
#else
    ln -s '$groupnames.shared_in' groupnames_shared_in.dat &&
#end if

echo 'remove.groups(
    #if $groupnames.source == "other":
        #if $group_in.is_of_type("mothur.groups"):
            group=groupnames_group_in.dat
        #else
            count=groupnames_group_in.dat
        #end if
        #if $groupnames.fasta_in:
            ,fasta=groupnames_fasta_in.dat
        #end if
        #if $groupnames.name_in:
            ,name=groupnames_name_in.dat
        #end if
        #if $groupnames.list_in:
            ,list=groupnames_list_in.dat
        #end if
        #if $groupnames.taxonomy_in:
            ,taxonomy=groupnames_taxonomy_in.dat
        #end if
        #if $column_in:
            ,column=groupnames_column_in.dat
        #end if
        #if $phylip_in:
            ,phylip=groupnames_phylip_in.dat
        #end if
    #else
        shared=groupnames_shared_in.dat
    #end if
    ,groups=${ str($groupnames.groups).replace(",","-") }
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <conditional name="groupnames">
            <param name="source" type="select" label="Select Input Type">
                <option value="shared">shared file</option>
                <option value="other">fasta, name, taxonomy, distance matrix or list with a group file or count table</option>
            </param>
            <when value="other">
                <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count table - Groups"/>
                <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
                    <options>
                        <filter type="data_meta" ref="group_in" key="groups"/>
                    </options>
                </param>
                <param name="fasta_in" type="data" format="mothur.align,fasta" optional="true" label="fasta - Fasta Sequences"/>
                <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
                <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
                <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
                <param name="phylip_in" type="data" format="mothur.lower.dist,mothur.square.dist" optional="true" label="phylip - Distance Matrix you would like to select distances from"
                    help="must be a phylip-formatted distance matrix"/>
                <param name="column_in" type="data" format="mothur.pair.dist" optional="true" label="column - Distance Matrix you would like to select distances from"
                    help="must be a column-formatted distance matrix"/>
            </when>
            <when value="shared">
                <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
                <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
                    <options>
                        <filter type="data_meta" ref="shared_in" key="groups"/>
                    </options>
                </param>
            </when>
        </conditional>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="fasta_out" format_source="fasta_in" from_work_dir="groupnames_fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
            <filter>groupnames['source'] == 'other' and groupnames['fasta_in']</filter>
        </data>
        <data name="group_out" format="mothur.groups" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
            <filter>groupnames['source'] == 'other' and groupnames['group_in'].ext == 'mothur.groups'</filter>
        </data>
        <data name="count_out" format="mothur.count_table" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.count_table">
            <filter>groupnames['source'] == 'other' and groupnames['group_in'].ext == 'mothur.count_table'</filter>
        </data>
        <data name="name_out" format="mothur.names" from_work_dir="groupnames_name_in*.pick.*" label="${tool.name} on ${on_string}: pick.names">
            <filter>groupnames['source'] == 'other' and groupnames['name_in']</filter>
        </data>
        <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="groupnames_taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
            <filter>groupnames['source'] == 'other' and groupnames['taxonomy_in']</filter>
        </data>
        <collection name="list_out" type="list" label="${tool.name} on ${on_string}: pick.list">
            <filter>groupnames['source'] == 'other' and groupnames['list_in']</filter>
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.list"/>
        </collection>
        <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: pick.shared">
            <filter>groupnames['source'] == 'shared'</filter>
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
        </collection>
        <data name="phylip_out" format_source="phylip_in" from_work_dir="groupnames_phylip_in*.pick.*" label="${tool.name} on ${on_string}: pick.phylip">
            <filter>groupnames['phylip_in']</filter>
        </data>
        <data name="column_out" format="mothur.pair.dist" from_work_dir="groupnames_column_in*.pick.*" label="${tool.name} on ${on_string}: pick.column">
            <filter>groupnames['column_in']</filter>
        </data>
    </outputs>
    <tests>
        <test><!-- test with shared file -->
            <param name="source" value="shared"/>
            <param name="shared_in" value="amazon.an.shared"/>
            <param name="groups" value="pasture"/>
            <output_collection name="shared_out" count="36">
                <element name="0.26" md5="c5043237225f0292ce1bfbd2766b96ea" ftype="mothur.shared"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with group file and fasta/names/list/taxonomy files -->
            <param name="source" value="other"/>
            <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
            <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
            <param name="name_in" value="amazon.names" ftype="mothur.names"/>
            <param name="list_in" value="amazon.an.list" ftype="mothur.list"/>
            <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <param name="groups" value="pasture"/>
            <output name="fasta_out" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
            <output name="taxonomy_out" md5="8fcaadcb5ad40873e270ad7e2cebe7fa" ftype="mothur.seq.taxonomy"/>
            <output name="group_out" md5="6d689ead98f3eb1af41f1a78386d0b50" ftype="mothur.groups"/>
            <output name="name_out" md5="55dbcadbb414d95bae8a282a93c10e63" ftype="mothur.names"/>
            <output_collection name="list_out" count="36">
                <element name="0.26" md5="3a92ef76cfdca6618b4016f14cbac5b8" ftype="mothur.list"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with distance matrices -->
            <param name="source" value="other"/>
            <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
            <param name="column_in" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
            <param name="phylip_in" value="amazon.dist" ftype="mothur.square.dist"/>
            <param name="groups" value="pasture"/>
            <output name="column_out" ftype="mothur.pair.dist">
                <assert_contents>
                    <expand macro="test-column-format"/>
                    <has_text text="U68589"/>
                </assert_contents>
            </output>
            <output name="phylip_out" ftype="mothur.square.dist">
                <assert_contents>
                    <expand macro="test-dist-format"/>
                    <has_text text="U68589"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The remove.groups_ command removes sequences from a specific group or set of groups from the following file types: fasta, name_, group_, list_, taxonomy_.

.. _name: https://www.mothur.org/wiki/Name_file
.. _group: https://www.mothur.org/wiki/Group_file
.. _list: https://www.mothur.org/wiki/List_file
.. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
.. _remove.groups: https://www.mothur.org/wiki/Remove.groups

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