Mercurial > repos > galaxyp > meta_proteome_analyzer
diff meta_proteome_analyzer.xml @ 2:ad3e9fdeabb7 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer commit 02be64dadeda429d0cf96806b7013820d087d8b9"
| author | galaxyp |
|---|---|
| date | Mon, 14 Dec 2020 21:18:06 +0000 |
| parents | 7fdfbf042ec6 |
| children | d8d23dfcf68b |
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--- a/meta_proteome_analyzer.xml Tue Apr 07 07:49:06 2020 -0400 +++ b/meta_proteome_analyzer.xml Mon Dec 14 21:18:06 2020 +0000 @@ -1,21 +1,36 @@ -<tool id="meta_proteome_analyzer" name="MetaProteomeAnalyzer" version="1.4.1+galaxy1"> +<tool id="meta_proteome_analyzer" name="MetaProteomeAnalyzer" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@"> <description> functional and taxonomic characterization of proteins </description> + <macros> + <token name="@TOOL_VERSION@">2.0.0</token> + <token name="@WRAPPER_VERSION@">0</token> + <xml name="test_output" token_name="" token_has_text=""> + <output name="output_PSMs"> + <assert_contents> + <has_text text="A2SPK1" /> + </assert_contents> + <yield/> + </output> + </xml> + </macros> <requirements> - <requirement type="package" version="1.4.1">mpa-portable</requirement> + <requirement type="package" version="@TOOL_VERSION@">mpa-portable</requirement> </requirements> - <command> + <stdio> + <regex match="Could not allocate metaspace" source="both" level="fatal_oom" description="Low space on device" /> + </stdio> + <command detect_errors="exit_code"> <![CDATA[ - cwd=`pwd` && mkdir -p output_dir && ## copy mpa conf dir to working dir jar_dir=`mpa-portable -get_jar_dir` && + cp -R \$jar_dir/conf . && ## echo the search engines to run - #set $search_engines = str($search_engines_options.engines).split(',') - echo "$search_engines_options.engines" && + #set $search_engines = str($engines).split(',') + echo "$engines" && echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}" && #for $mgf in $peak_lists: @@ -29,8 +44,8 @@ ###################### ## MPA ## ###################### - mpa-portable de.mpa.cli.CmdLineInterface -Djava.awt.headless=true -Xmx2048m - -spectrum_files \$cwd + mpa-portable de.mpa.cli.CmdLineInterface --exec_dir=exec_dir -Xmx2048m + -spectrum_files "\$(pwd)" -database input_database.fasta -missed_cleav $missed_cleavages -prec_tol ${precursor_options.prec_tol}${precursor_options.prec_tol_units} @@ -38,10 +53,18 @@ -xtandem #if 'X!Tandem' in $search_engines then 1 else 0# -comet #if 'Comet' in $search_engines then 1 else 0# -msgf #if 'MSGF' in $search_engines then 1 else 0# + -generate_metaproteins $generate_metaproteins + -iterative_search $iterative_search + -fragment_method $fragment_method + -peptide_index $peptide_index + -fdr_threshold $fdr_threshold + -semi_tryptic $semi_tryptic -output_folder output_dir -threads "\${GALAXY_SLOTS:-12}" && - mv ./output_dir/*_metaproteins.csv metaproteins.csv && - mv ./output_dir/*_metaprotein_taxa.csv metaprotein_taxa.csv && + #if $generate_metaproteins == "1" + mv ./output_dir/*_metaproteins.csv metaproteins.csv && + mv ./output_dir/*_metaprotein_taxa.csv metaprotein_taxa.csv && + #end if mv ./output_dir/*_peptides.csv peptides.csv && mv ./output_dir/*_proteins.csv proteins.csv && mv ./output_dir/*_psms.csv psms.csv && @@ -67,25 +90,22 @@ help="Provide error value for fragment ions, based on instrument used"/> </section> <!-- Search Engine Selection --> - <section name="search_engines_options" expanded="false" title="Search Engine Options"> - <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> - <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help> - <option value="X!Tandem" selected="True">X!Tandem</option> - <option value="MSGF">MS-GF+</option> - <option value="Comet">Comet</option> - </param> - </section> - -<!-- --generate_metaproteins Turn meta-protein generation (aka. protein grouping) on or off (1: on, 0: off, default is '1'). --peptide_rule The peptide rule chosen for meta-protein generation (-1: off, 0: share-one-peptide, 1: shared-peptide-subset, default is '0'). --cluster_rule The sequence cluster rule chosen for meta-protein generation (-1: off, 0: UniRef100, 1: UniRef90, 2: UniRef50, default is '-1'). --taxonomy_rule The taxonomy rule chosen for meta-protein generation (-1: off, 0: on superkingdom or lower, 1: on kingdom or lower, 2: on phylum or lower, 3: on class or lower, 4: on order or lower, 5: on family or lower, 6: on genus or lower, 7: on species or lower, 8: on subspecies, default is '-1'). --iterative_search Turn iterative (aka. two-step) searching on or off (1: on, 0: off, default is '0'). --fdr_threshold The applied FDR threshold for filtering the results (default is 0.05 == 5% FDR). ---> - - + <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> + <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help> + <option value="X!Tandem" selected="True">X!Tandem</option> + <option value="MSGF">MS-GF+</option> + <option value="Comet">Comet</option> + </param> + <param argument="-generate_metaproteins" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Meta-protein generation" help="aka. protein grouping"/> + <param argument="-iterative_search" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Iterative searching" help="aka. two-step searching"/> + <param argument="-semi_tryptic" type="boolean" truevalue="1" falsevalue="0" checked="false" label="" help="Semi-tryptic cleavage"/> + <param argument="-fragment_method" type="select" label="Fragmentation method" help="for the MS instrument"> + <option value="1" selected="true">CID</option> + <option value="2">HCD</option> + <option value="3">ETD</option> + </param> + <param argument="-peptide_index" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Peptide indexing (of FASTA database)" help=""/> + <param argument="-fdr_threshold" type="float" value="0.05" min="0" max="1" label="FDR threshold for filtering" help=""/> </inputs> <outputs> <data format="tabular" name="output_proteins" from_work_dir="proteins.csv" label="${tool.name} on ${on_string}: proteins"> @@ -113,12 +133,14 @@ </actions> </data> <data format="tabular" name="output_metaproteins" from_work_dir="metaproteins.csv" label="${tool.name} on ${on_string}: metaproteins"> + <filter>generate_metaproteins</filter> <actions> <action name="comment_lines" type="metadata" default="1" /> <action name="column_names" type="metadata" default="Meta-Protein_Num,Meta-Protein_Accession,Meta-Protein_Description,Meta-Protein_Taxonomy,Meta-Protein_UniRef100,Meta-Protein_UniRef90,Meta-Protein_UniRef50,Meta-Protein_KO,Meta-Protein_EC,Peptide_Count,Spectral_Count,Proteins,Peptides" /> </actions> </data> <data format="tabular" name="output_metaprotein_taxa" from_work_dir="metaprotein_taxa.csv" label="${tool.name} on ${on_string}: metaprotein_taxa"> + <filter>generate_metaproteins</filter> <actions> <action name="comment_lines" type="metadata" default="1" /> <action name="column_names" type="metadata" default="Unclassified,Superkingdom,Kingdom,Phylum,Class,Order,Family,Genus,Species,Subspecies,Num_Peptides,Spectral_Count" /> @@ -126,7 +148,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="6"> <param name="peak_lists" value="Test416Ebendorf.mgf" ftype="mgf"/> <param name="input_database" value="searchdb.fa" ftype="fasta"/> <param name="missed_cleavages" value="2"/> @@ -134,11 +156,36 @@ <param name="prec_tol" value="10"/> <param name="frag_tol" value="0.5"/> <param name="engines" value="X!Tandem,MSGF,Comet"/> - <output name="output_PSMs"> - <assert_contents> - <has_text text="A2SPK1" /> + <expand macro="test_output" name="output_proteins" has_text="B8GJQ7"/> + <expand macro="test_output" name="output_peptides" has_text="B8GJQ7"/> + <expand macro="test_output" name="output_PSMs" has_text="B8GJQ7"> + <assert_contents> + <has_text text="X!Tandem" /> </assert_contents> - </output> + </expand> + <expand macro="test_output" name="output_spectrum_ids" has_text="B8GJQ7"/> + <expand macro="test_output" name="output_metaproteins" has_text="B8GJQ7"/> + <expand macro="test_output" name="output_metaprotein_taxa" has_text="Unknown Superkingdomq"/> + </test> + <test expect_num_outputs="4"> + <param name="peak_lists" value="Test416Ebendorf.mgf" ftype="mgf"/> + <param name="input_database" value="searchdb.fa" ftype="fasta"/> + <param name="missed_cleavages" value="2"/> + <param name="prec_tol" value="ppm"/> + <param name="prec_tol" value="10"/> + <param name="frag_tol" value="0.5"/> + <param name="engines" value="MSGF,Comet"/> + <param name="generate_metaproteins" value="0"/> + <expand macro="test_output" name="output_proteins" has_text="B8GJQ7"/> + <expand macro="test_output" name="output_peptides" has_text="B8GJQ7"/> + <expand macro="test_output" name="output_PSMs" has_text="B8GJQ7"> + <assert_contents> + <not_has_text text="X!Tandem" /> + </assert_contents> + </expand> + <expand macro="test_output" name="output_spectrum_ids" has_text="B8GJQ7"/> + <expand macro="test_output" name="output_metaproteins" has_text="B8GJQ7"/> + <expand macro="test_output" name="output_metaprotein_taxa" has_text="Unknown Superkingdomq"/> </test> </tests> <help> @@ -163,10 +210,6 @@ * spectrum_ids * metaproteins * metaprotein_taxa - - ------- - </help> <citations> <citation type="doi">10.1021/pr501246w</citation>