comparison genenotebook_build.xml @ 2:5a6050937cb9 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014

1:f415e44e71de

    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
@START_GNB@

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

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

        #if $annot.blast_cond.blast_choice == "yes":
            genoboo add blast @CONNECT_INFO@
                --format 'xml'
                --algorithm '${annot.blast_cond.algorithm}'
                --matrix '${annot.blast_cond.matrix}'
                --database '${annot.blast_cond.database}'
                '${annot.blast_cond.blast}';
        #end if

        #for exp in $annot.expression:
            genoboo add transcriptome @CONNECT_INFO@
                --sample-name '${exp.sample_name}'

                <param name="eggnog" label="EggNOG-Mapper results" optional="true" type="data" format="tsv" />

                <conditional name="blast_cond">
                    <param name="blast_choice" type="select" label="Import Blast or Diamond results">
                        <option value="no" selected="true">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                        <param name="blast" label="Blast or Diamond results" optional="false" type="data" format="xml" />
                        <param argument="--algorithm" label="Algorithm" optional="false" type="text" help="e.g. blastx, blastp" />
                        <param argument="--matrix" label="Matrix" optional="false" type="text" help="e.g. BLOSUM90, BLOSUM80, PAM100" />
                        <param argument="--database" label="database" optional="false" type="text" help="e.g. Non-reundant protein sequences (nr)" />
                    </when>
                </conditional>

            </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="addAnnotation 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">

            </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="addAnnotation succesfully inserted 5 elements" />
                <has_text text="addInterproscan succesfully inserted 5 elements" />
                <has_text text="addEggnog succesfully inserted 4 elements" />
            </assert_stdout>
        </test>
        <test>
            <repeat name="genomes">

                        <param name="re_protein_capture" value="^(.*?)-T([0-9]+)$" />
                        <param name="re_protein" value="$1-P$2" />
                    </conditional>

                    <conditional name="blast_cond">
                        <param name="blast_choice" value="yes"/>
                        <param name="blast" value="blast.xml" ftype="xml" />
                        <param name="algorithm" value="blastx" />
                        <param name="matrix" value="BLOSUM80" />
                        <param name="database" value="Non-reundant garbage (nrg)" />
                    </conditional>

                <has_text text="addAnnotation succesfully inserted 5 elements" />
                <has_text text="addSimilarSequence succesfully inserted 1 elements" />
                <has_text text="addTranscriptome succesfully inserted 1 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.

2:5a6050937cb9

    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
@START_GNB@

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

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

        #if $annot.blast_cond.blast_choice == "blast":
            genoboo add blast @CONNECT_INFO@
                --format 'xml'
                --algorithm '${annot.blast_cond.algorithm}'
                --matrix '${annot.blast_cond.matrix}'
                --database '${annot.blast_cond.database}'
                '${annot.blast_cond.blast}';
        #elif $annot.blast_cond.blast_choice == "diamond":
            genoboo add diamond @CONNECT_INFO@
                --format 'xml'
                --algorithm '${annot.blast_cond.algorithm}'
                --matrix '${annot.blast_cond.matrix}'
                --database '${annot.blast_cond.database}'
                '${annot.blast_cond.diamond}';
        #end if

        #for exp in $annot.expression:
            genoboo add transcriptome @CONNECT_INFO@
                --sample-name '${exp.sample_name}'

                <param name="eggnog" label="EggNOG-Mapper results" optional="true" type="data" format="tsv" />

                <conditional name="blast_cond">
                    <param name="blast_choice" type="select" label="Import Blast or Diamond results">
                        <option value="no" selected="true">No</option>
                        <option value="blast">Blast</option>
                        <option value="diamond">Diamond</option>
                    </param>
                    <when value="no" />
                    <when value="blast">
                        <param name="blast" label="Blast results (xml)" optional="false" type="data" format="xml" />
                        <param argument="--algorithm" label="Algorithm" optional="false" type="text" help="e.g. blastx, blastp" />
                        <param argument="--matrix" label="Matrix" optional="false" type="text" help="e.g. BLOSUM90, BLOSUM80, PAM100" />
                        <param argument="--database" label="database" optional="false" type="text" help="e.g. Non-reundant protein sequences (nr)" />
                    </when>
                    <when value="diamond">
                        <param name="diamond" label="Diamond results (xml)" optional="false" type="data" format="xml" />
                        <param argument="--algorithm" label="Algorithm" optional="false" type="text" help="e.g. blastx, blastp" />
                        <param argument="--matrix" label="Matrix" optional="false" type="text" help="e.g. BLOSUM90, BLOSUM80, PAM100" />
                        <param argument="--database" label="database" optional="false" type="text" help="e.g. Non-reundant protein sequences (nr)" />
                    </when>
                </conditional>

            </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="addAnnotation succesfully inserted 5 elements" />
                <has_text text="addInterproscan succesfully inserted 3 elements" />
            </assert_stdout>
        </test>
        <test>
            <param name="existing" value="output/genome.tar.bz2" />
            <repeat name="genomes">

            </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="addAnnotation succesfully inserted 5 elements" />
                <has_text text="addInterproscan succesfully inserted 3 elements" />
                <has_text text="addEggnog succesfully inserted 4 elements" />
            </assert_stdout>
        </test>
        <test>
            <repeat name="genomes">

                        <param name="re_protein_capture" value="^(.*?)-T([0-9]+)$" />
                        <param name="re_protein" value="$1-P$2" />
                    </conditional>

                    <conditional name="blast_cond">
                        <param name="blast_choice" value="blast"/>
                        <param name="blast" value="blast.xml" ftype="xml" />
                        <param name="algorithm" value="blastx" />
                        <param name="matrix" value="BLOSUM80" />
                        <param name="database" value="Non-reundant garbage (nrg)" />
                    </conditional>

                <has_text text="addAnnotation succesfully inserted 5 elements" />
                <has_text text="addSimilarSequence succesfully inserted 1 elements" />
                <has_text text="addTranscriptome 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" />

                    <conditional name="prot_naming">
                        <param name="method" value="regex"/>
                        <param name="re_protein_capture" value="^(.*?)-T([0-9]+)$" />
                        <param name="re_protein" value="$1-P$2" />
                    </conditional>

                    <conditional name="blast_cond">
                        <param name="blast_choice" value="diamond"/>
                        <param name="diamond" value="blast.xml" ftype="xml" />
                        <param name="algorithm" value="blastx" />
                        <param name="matrix" value="BLOSUM62" />
                        <param name="database" value="Non-reundant garbage (nrg)" />
                    </conditional>

                    <repeat name="expression">
                        <param name="counts" value="exp.tsv" ftype="tsv" />
                        <param name="sample_name" value="Sample1_rep1" />
                        <param name="replica_group" value="Sample1" />
                        <param name="sample_description" value="Pointless experiment" />
                    </repeat>
                </repeat>
            </repeat>
            <output name="gnb_db" file="output/genome_annot_ips_en_bl_exp.tar.bz2" compare="sim_size" delta="15000" />
            <assert_stdout>
                <has_text text="addGenome succesfully inserted 1 elements" />
                <has_text text="addAnnotation succesfully inserted 5 elements" />
                <has_text text="addSimilarSequence succesfully inserted 1 elements" />
                <has_text text="addTranscriptome succesfully inserted 1 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.