view sixgill_merge.xml @ 0:cf8eee8343fb draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty

<tool id="sixgill_merge" name="sixgill merge" version="@VERSION@.0">
    <description>metapeptide databases</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <version_command>sixgill_merge --version</version_command>
    <command><![CDATA[
        sixgill_merge 
            --nogzipout
            --out=metapeptides_db_output.tsv
            #for ($i,$metapeptide_db) in enumerate($metapeptide_dbs)
                "$metapeptide_db"
            #end for
            #if 'fa' in str($output_choice):
                &&
                sixgill_makefasta --type=aa --out="metapeptides_fa_output.fa" "metapeptides_db_output.tsv"
            #end if
    ]]></command>
    <inputs>
        <param name="metapeptide_dbs" type="data" format="tabular" multiple="true" optional="false" label="metapeptide databases" 
         help="Can be generated with sixgill_build"/>
        <param name="output_choice" type="select" multiple="true" optional="false" label="select outputs">
            <option value="db" selected="true">metapeptide database</option>
            <option value="fa">metapeptide protein fasta</option>
        </param>
    </inputs>
    <outputs>
        <data name="output_db" format="tabular" label="${tool.name} on ${on_string}: metapeptides.tsv" from_work_dir="metapeptides_db_output.tsv">
            <filter>'db' in output_choice</filter>
            <actions>
                <action name="comment_lines" type="metadata" default="1" />
                <action name="column_names" type="metadata" default="sequence,length,min_qualscore,partial_orf_length,metagene_score,read_ids" />
            </actions>
        </data>
        <data name="output_fa" format="fasta" label="${tool.name} on ${on_string}: metapeptides.fa" from_work_dir="metapeptides_fa_output.fa">
            <filter>'fa' in output_choice</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="metapeptide_dbs" ftype="tabular" 
                   value="testdb_metagene.metapeptides.tsv,testdb_nometagene.metapeptides.tsv"/>
            <output name="output_db">
                <assert_contents>
                    <has_text text="DLRILLRERLVAGDSDEAAVDFIVDR" />
                    <has_text text="YHNFEGYRWR" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
usage: sixgill_merge [-h] --out OUT [--debug]
                     metapeptidedbfiles [metapeptidedbfiles ...]

Merge multiple metapeptide database files into a single metapeptide database.
Optionally, filter simultaneously.

positional arguments:
  metapeptidedbfiles  input metapeptide database files

optional arguments:
  -h, --help          show this help message and exit
  --out OUT           output file
  --debug             Enable debug logging

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