comparison orthofinder_only_groups.xml @ 1:918d141a166b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca

0:bfb20dbe1309

<tool name="OrthoFinder OnlyGroups" id="orthofinder_onlygroups" version="1.1.4">
    <description>finds orthogroups in a set of proteomes</description>  
    <requirements>
        <requirement type="package" version="1.1.4">orthofinder</requirement>
    </requirements>
    <command>
    <![CDATA[
        ## prepare inputs
        #if $init.start=="fasta":
            #set $infiles = ""
            #for $input in $init.input_fasta
                ln -s '$input' '$input.element_identifier' &&
                #set $infiles = $infiles + str($input.element_identifier) + ","
            #end for
            #set $infiles = $infiles[:-1]
        #elif $init.start=="blast":
            #set $infilesbl = ""

        <data format="txt" name="SequenceIDs" label="SequencesIDs.txt" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" >
            <filter>init['start']=="fasta" and init['keepblastout']</filter>
        </data>
    </outputs>
    <tests>
        <!-- test orthofinder -f -og -->
        <test>
            <conditional name="init">
                <param name="start" value="fasta" />
                <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />

                    <has_text text="Number of orthogroups"/>
                    <has_text text="Number of genes"/>
                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
            <output name="SpeciesIDs" value="inputs/blastids/SpeciesIDs.txt" />
            <output name="SequenceIDs" value="inputs/blastids/SequenceIDs.txt" />
            <output_collection name="wdfasta" type="list" count="4"/>
            <output_collection name="wdblast" type="list" count="16"/>
        </test>
        

            <output name="specs_overlap" value="results_fromblast/Orthogroups_SpeciesOverlaps.csv"/>
            <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.csv"/>
            <output name="stat_overall" value="results_fromblast/Statistics_Overall.csv" lines_diff="2"/>
            <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.csv"/>
        </test>
    </tests>    
    <help>
======================
OrthoFinder OnlyGroups
======================

1:918d141a166b

<tool name="OrthoFinder OnlyGroups" id="orthofinder_onlygroups" version="1.1.4">
    <description>finds orthogroups in a set of proteomes</description>
    <requirements>
        <requirement type="package" version="1.1.4">orthofinder</requirement>
    </requirements>
    <command>
    <![CDATA[
        ## prepare inputs
        #if $init.start=="fasta":
            #set $infiles = ""
            #for $input in $init.input_fasta
                ln -s '$input' '${input.element_identifier}.fasta' &&
                #set $infiles = $infiles + str($input.element_identifier) + ","
            #end for
            #set $infiles = $infiles[:-1]
        #elif $init.start=="blast":
            #set $infilesbl = ""

        <data format="txt" name="SequenceIDs" label="SequencesIDs.txt" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" >
            <filter>init['start']=="fasta" and init['keepblastout']</filter>
        </data>
    </outputs>
    <tests>
        <!-- test orthofinder -f . -og when input files has no extension fasta/faa/fa ... -->
        <test>
            <conditional name="init">
                <param name="start" value="fasta" />
                <param name="input_fasta" ftype="fasta" value="inputs/no_fa_ext/AcAcaud_trinity,inputs/no_fa_ext/AmAmphi_trinity,inputs/no_fa_ext/ApApomp_trinity,inputs/no_fa_ext/AsAsp1_trinity" />
                <param name="keepblastout" value="no" />
            </conditional>
            <param name="inflation" value="1.5" />
            <output name="specs_overlap">
                <assert_contents>
                    <has_text text="AcAcaud_trinity"/>
                    <has_text text="AmAmphi_trinity"/>
                    <has_text text="ApApomp_trinity"/>
                    <has_text text="AsAsp1_trinity"/>
                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
            <output name="unassigned_genes">
                <assert_contents>
                    <has_text text="AcAcaud_trinity"/>
                    <has_text text="AmAmphi_trinity"/>
                    <has_text text="ApApomp_trinity"/>
                    <has_text text="AsAsp1_trinity"/>
                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
            <output name="stat_overall">
                <assert_contents>
                    <has_text text="Number of genes in orthogroups"/>
                    <has_text text="Number of unassigned genes"/>
                    <has_text text="Percentage of orthogroups"/>
                    <has_text text="Number of orthogroups"/>
                    <has_text text="Number of genes"/>
                    <has_text text="G50 (assigned genes)"/>
                    <has_text text="G50 (all genes)"/>
                    <has_text text="O50 (assigned genes)"/>
                    <has_text text="O50 (all genes)"/>
                </assert_contents>
            </output>
            <output name="stat_specs">
                <assert_contents>
                    <has_text text="AcAcaud_trinity"/>
                    <has_text text="AmAmphi_trinity"/>
                    <has_text text="ApApomp_trinity"/>
                    <has_text text="AsAsp1_trinity"/>
                    <has_text text="Number of genes per-species in orthogroup"/>
                    <has_text text="Percentage of orthogroups"/>
                    <has_text text="Number of orthogroups"/>
                    <has_text text="Number of genes"/>
                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
        </test>
        <!-- test orthofinder -f -og -->
        <test>
            <conditional name="init">
                <param name="start" value="fasta" />
                <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />

                    <has_text text="Number of orthogroups"/>
                    <has_text text="Number of genes"/>
                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
            <output name="SequenceIDs" value="inputs/blastids/SequenceIDs.txt" />
            <output_collection name="wdfasta" type="list" count="4"/>
            <output_collection name="wdblast" type="list" count="16"/>
        </test>
        

            <output name="specs_overlap" value="results_fromblast/Orthogroups_SpeciesOverlaps.csv"/>
            <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.csv"/>
            <output name="stat_overall" value="results_fromblast/Statistics_Overall.csv" lines_diff="2"/>
            <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.csv"/>
        </test>
    </tests>
    <help>
======================
OrthoFinder OnlyGroups
======================