annotate genenotebook_build.xml @ 0:22f22c3e81bf draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b

<?xml version="1.0"?>
<tool id="genenotebook_build" name="Build a GeneNoteBook" version="@WRAPPER_VERSION@" profile="21.05">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
@START_GNB@

#for genome in $genomes:
    genenotebook add genome @CONNECT_INFO@ --name '${genome.name}' '${genome.genome}';

    #for annot in $genome.annots:
        genenotebook add annotation @CONNECT_INFO@ --genome-name '${genome.name}' '${annot.annotation}';
        #if $annot.interproscan:
            genenotebook add interproscan @CONNECT_INFO@ --format
            #if $annot.interproscan.is_of_type('gff3'):
                gff3
            #else:
                tsv
            #end if
            '${annot.interproscan}';
        #end if

        #if $annot.eggnog:
            genenotebook add eggnog @CONNECT_INFO@ '${annot.eggnog}';
        #end if
    #end for
#end for

@ZIP_GNB@
    ]]></command>
    <inputs>
        <param name="existing" type="data" format="genenotebook" optional="true" label="Load data in an existing GeneNoteBook database" help="Leave empty to start a new database from scratch" />
        <repeat name="genomes" title="Genomes">
            <param argument="--name" label="Name" type="text" help="Reference genome name" />
            <param name="genome" label="Genome sequence" type="data" format="fasta" />
            <repeat name="annots" title="Annotations">
                <param name="annotation" label="Annotation" type="data" format="gff3" />
                <param name="interproscan" label="InterProScan results" optional="true" type="data" format="tsv,gff3" />
                <param name="eggnog" label="EggNOG-Mapper results" optional="true" type="data" format="tsv" />
            </repeat>
        </repeat>
    </inputs>
    <outputs>
        <data format="genenotebook" name="gnb_db" label="GeneNoteBook on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <repeat name="genomes">
                <param name="name" value="Test org" />
                <param name="genome" value="genome.fa" />
            </repeat>
            <output name="gnb_db" file="output/genome.tar.bz2" compare="sim_size" />
            <assert_stdout>
                <has_text text="addGenome succesfully inserted 1 elements" />
            </assert_stdout>
        </test>
        <test>
            <repeat name="genomes">
                <param name="name" value="Test org 2" />
                <param name="genome" value="genome.fa" />
                <repeat name="annots">
                    <param name="annotation" value="annot.gff" />
                </repeat>
            </repeat>
            <output name="gnb_db" file="output/genome_annot.tar.bz2" compare="sim_size" />
            <assert_stdout>
                <has_text text="addGenome succesfully inserted 1 elements" />
                <has_text text="addAnnotationTrack succesfully inserted 5 elements" />
            </assert_stdout>
        </test>
        <test>
            <repeat name="genomes">
                <param name="name" value="Test org 2" />
                <param name="genome" value="genome.fa" />
                <repeat name="annots">
                    <param name="annotation" value="annot.gff" />
                    <param name="interproscan" value="interproscan.tsv" ftype="tsv" />
                </repeat>
            </repeat>
            <output name="gnb_db" file="output/genome_annot_ips.tar.bz2" compare="sim_size" />
            <assert_stdout>
                <has_text text="addGenome succesfully inserted 1 elements" />
                <has_text text="addAnnotationTrack succesfully inserted 5 elements" />
                <has_text text="addInterproscan succesfully inserted 5 elements" />
            </assert_stdout>
        </test>
        <test>
            <param name="existing" value="output/genome.tar.bz2" />
            <repeat name="genomes">
                <param name="name" value="Test org 2" />
                <param name="genome" value="genome.fa" />
            </repeat>
            <output name="gnb_db" file="output/genome_reload.tar.bz2" compare="sim_size" />
            <assert_stdout>
                <has_text text="addGenome succesfully inserted 1 elements" />
            </assert_stdout>
        </test>
        <test>
            <repeat name="genomes">
                <param name="name" value="Test org 2" />
                <param name="genome" value="genome.fa" />
                <repeat name="annots">
                    <param name="annotation" value="annot.gff" />
                    <param name="interproscan" value="interproscan.tsv" ftype="tsv" />
                    <param name="eggnog" value="eggnog.tsv" ftype="tsv" />
                </repeat>
            </repeat>
            <output name="gnb_db" file="output/genome_annot_ips_en.tar.bz2" compare="sim_size" delta="15000" />
            <assert_stdout>
                <has_text text="addGenome succesfully inserted 1 elements" />
                <has_text text="addAnnotationTrack succesfully inserted 5 elements" />
                <has_text text="addInterproscan succesfully inserted 5 elements" />
                <has_text text="addEggnog succesfully inserted undefined elements" />
            </assert_stdout>
        </test>
    </tests>
    <help><![CDATA[
Build a GeneNoteBook by loading data into a MongoDB database. The resulting dataset can then be displayed with the "View a GeneNoteBook" interactive tool (to be written).

The resulting GeneNoteBook will contain the default user accounts created on the first launch. You are responsible to change them if you ever want to put your result online.
    ]]></help>
    <expand macro="citation" />
</tool>