comparison orthofinder_only_groups.xml @ 6:0ff17c7a18cd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 278a22cd0f7b47a958647e1e6dcf4bf56c4dcbbc"

5:974d8c28e586

<tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@">
    <description>finds orthogroups in a set of proteomes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>

        <collection name="wdfasta" type="list" label="OrthoFinder on ${on_string}: fasta from blast" >
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fa" directory="results/WorkingDirectory/fa" format="fasta" />
            <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
        </collection>
        <data format="txt" name="SpeciesIDs" label="OrthoFinder on ${on_string}: SpeciesIDs" from_work_dir="results/WorkingDirectory/SpeciesIDs.txt" >
            <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']"</filter>
        </data>
        <data format="txt" name="SequenceIDs" label="OrthoFinder on ${on_string}: SequencesIDs" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" >
            <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
        </data>

            <filter>trees['run_mode'] == "full" and output_duplications</filter>
        </collection>
    </outputs>
    <tests>
        <!-- no trees + diamond + input files have 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" />
                <conditional name="search">
                    <param name="search_program" value="diamond"/>

                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
        </test>
        <!-- no trees + diamond + input files have extension fasta/faa/fa -->
        <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" />
                <conditional name="search">
                    <param name="search_program" value="diamond"/>

                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
        </test>
        <!-- no trees + diamond + input files have extension fasta/faa/fa + keep blast out -->
        <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" />
                <conditional name="search">
                    <param name="search_program" value="blast"/>

            <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>
        <!-- no trees + blast + input files have extension fasta/faa/fa-->
        <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" />
                <conditional name="search">
                    <param name="search_program" value="blast"/>

                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
        </test>
        <!-- no trees + uploaded blast-->
        <test>
            <conditional name="init">
                <param name="start" value="blast" />
                <param name="input_blast_out">
                    <collection type="list">
                        <element name="Blast0_0.txt" value="inputs/blastout/Blast0_0.txt"/>

            <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.tsv"/>
            <output name="stat_overall" value="results_fromblast/Statistics_Overall.tsv" lines_diff="2"/>
            <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.tsv"/>
        </test>
        <!-- full mode + diamond + input files have extension fasta/faa/fa -->
        <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" />
                <conditional name="search">
                    <param name="search_program" value="diamond"/>

                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
            <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/>
            <output_collection name="genetrees" type="list" count="0"/>
            <output_collection name="resolved_trees" type="list" count="0"/>
        </test>
        <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications -->
        <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" />
                <conditional name="search">
                    <param name="search_program" value="diamond"/>

            <output name="duplications_per_species_tree_node" value="results/Duplications_per_Species_Tree_Node.tsv" compare="sim_size"/>
            <output_collection name="genetrees" type="list" count="325"/>
            <output_collection name="resolved_trees" type="list" count="325"/>
        </test>
        <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
        <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" />
                <conditional name="search">
                    <param name="search_program" value="diamond"/>

                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
        </test>
        <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
        <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" />
                <conditional name="search">
                    <param name="search_program" value="diamond"/>

6:0ff17c7a18cd

<tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>finds orthogroups in a set of proteomes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>

        <collection name="wdfasta" type="list" label="OrthoFinder on ${on_string}: fasta from blast" >
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fa" directory="results/WorkingDirectory/fa" format="fasta" />
            <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
        </collection>
        <data format="txt" name="SpeciesIDs" label="OrthoFinder on ${on_string}: SpeciesIDs" from_work_dir="results/WorkingDirectory/SpeciesIDs.txt" >
            <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
        </data>
        <data format="txt" name="SequenceIDs" label="OrthoFinder on ${on_string}: SequencesIDs" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" >
            <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
        </data>

            <filter>trees['run_mode'] == "full" and output_duplications</filter>
        </collection>
    </outputs>
    <tests>
        <!-- no trees + diamond + input files have no extension fasta/faa/fa -->
        <test expect_num_outputs="6">
            <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" />
                <conditional name="search">
                    <param name="search_program" value="diamond"/>

                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
        </test>
        <!-- no trees + diamond + input files have extension fasta/faa/fa -->
        <test expect_num_outputs="6">
            <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" />
                <conditional name="search">
                    <param name="search_program" value="diamond"/>

                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
        </test>
        <!-- no trees + diamond + input files have extension fasta/faa/fa + keep blast out -->
        <test expect_num_outputs="10">
            <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" />
                <conditional name="search">
                    <param name="search_program" value="blast"/>

            <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>
        <!-- no trees + blast + input files have extension fasta/faa/fa-->
        <test expect_num_outputs="6">
            <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" />
                <conditional name="search">
                    <param name="search_program" value="blast"/>

                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
        </test>
        <!-- no trees + uploaded blast-->
        <test expect_num_outputs="6">
            <conditional name="init">
                <param name="start" value="blast" />
                <param name="input_blast_out">
                    <collection type="list">
                        <element name="Blast0_0.txt" value="inputs/blastout/Blast0_0.txt"/>

            <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.tsv"/>
            <output name="stat_overall" value="results_fromblast/Statistics_Overall.tsv" lines_diff="2"/>
            <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.tsv"/>
        </test>
        <!-- full mode + diamond + input files have extension fasta/faa/fa -->
        <test expect_num_outputs="9">
            <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" />
                <conditional name="search">
                    <param name="search_program" value="diamond"/>

                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
            <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/>
            <output_collection name="genetrees" type="list" count="0"/>
        </test>
        <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications -->
        <test expect_num_outputs="14">
            <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" />
                <conditional name="search">
                    <param name="search_program" value="diamond"/>

            <output name="duplications_per_species_tree_node" value="results/Duplications_per_Species_Tree_Node.tsv" compare="sim_size"/>
            <output_collection name="genetrees" type="list" count="325"/>
            <output_collection name="resolved_trees" type="list" count="325"/>
        </test>
        <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
        <test expect_num_outputs="6">
            <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" />
                <conditional name="search">
                    <param name="search_program" value="diamond"/>

                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
        </test>
        <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
        <test expect_num_outputs="9">
            <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" />
                <conditional name="search">
                    <param name="search_program" value="diamond"/>