| Previous changeset 1:7fdfbf042ec6 (2020-04-07) Next changeset 3:d8d23dfcf68b (2021-01-03) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer commit 02be64dadeda429d0cf96806b7013820d087d8b9" |
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modified:
meta_proteome_analyzer.xml |
| b |
| diff -r 7fdfbf042ec6 -r ad3e9fdeabb7 meta_proteome_analyzer.xml --- 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 |
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| b'@@ -1,21 +1,36 @@\n-<tool id="meta_proteome_analyzer" name="MetaProteomeAnalyzer" version="1.4.1+galaxy1">\n+<tool id="meta_proteome_analyzer" name="MetaProteomeAnalyzer" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@">\n <description>\n functional and taxonomic characterization of proteins\n </description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">2.0.0</token>\n+ <token name="@WRAPPER_VERSION@">0</token>\n+ <xml name="test_output" token_name="" token_has_text="">\n+ <output name="output_PSMs">\n+ <assert_contents>\n+ <has_text text="A2SPK1" />\n+ </assert_contents>\n+ <yield/>\n+ </output>\n+ </xml>\n+ </macros>\n <requirements>\n- <requirement type="package" version="1.4.1">mpa-portable</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">mpa-portable</requirement>\n </requirements>\n- <command>\n+ <stdio>\n+ <regex match="Could not allocate metaspace" source="both" level="fatal_oom" description="Low space on device" />\n+ </stdio>\n+ <command detect_errors="exit_code">\n <![CDATA[\n- cwd=`pwd` &&\n mkdir -p output_dir &&\n ## copy mpa conf dir to working dir\n jar_dir=`mpa-portable -get_jar_dir` &&\n+\n cp -R \\$jar_dir/conf . &&\n \n ## echo the search engines to run\n- #set $search_engines = str($search_engines_options.engines).split(\',\')\n- echo "$search_engines_options.engines" &&\n+ #set $search_engines = str($engines).split(\',\')\n+ echo "$engines" &&\n echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}" &&\n \n #for $mgf in $peak_lists:\n@@ -29,8 +44,8 @@\n ######################\n ## MPA ##\n ######################\n- mpa-portable de.mpa.cli.CmdLineInterface -Djava.awt.headless=true -Xmx2048m\n- -spectrum_files \\$cwd\n+ mpa-portable de.mpa.cli.CmdLineInterface --exec_dir=exec_dir -Xmx2048m\n+ -spectrum_files "\\$(pwd)"\n -database input_database.fasta\n -missed_cleav $missed_cleavages\n -prec_tol ${precursor_options.prec_tol}${precursor_options.prec_tol_units}\n@@ -38,10 +53,18 @@\n -xtandem #if \'X!Tandem\' in $search_engines then 1 else 0#\n -comet #if \'Comet\' in $search_engines then 1 else 0#\n -msgf #if \'MSGF\' in $search_engines then 1 else 0#\n+ -generate_metaproteins $generate_metaproteins\n+ -iterative_search $iterative_search\n+ -fragment_method $fragment_method\n+ -peptide_index $peptide_index\n+ -fdr_threshold $fdr_threshold\n+ -semi_tryptic $semi_tryptic\n -output_folder output_dir\n -threads "\\${GALAXY_SLOTS:-12}" &&\n- mv ./output_dir/*_metaproteins.csv metaproteins.csv &&\n- mv ./output_dir/*_metaprotein_taxa.csv metaprotein_taxa.csv &&\n+ #if $generate_metaproteins == "1"\n+ mv ./output_dir/*_metaproteins.csv metaproteins.csv &&\n+ mv ./output_dir/*_metaprotein_taxa.csv metaprotein_taxa.csv &&\n+ #end if\n mv ./output_dir/*_peptides.csv peptides.csv &&\n mv ./output_dir/*_proteins.csv proteins.csv &&\n mv ./output_dir/*_psms.csv psms.csv &&\n@@ -67,25 +90,22 @@\n help="Provide error value for fragment ions, based on instrument used"/>\n </section>\n <!-- Search Engine Selection -->\n- <section name="search_engines_options" expanded="false" title="Search Engine Options">\n- <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">\n- <help>Comet and Tide shouldn\'t both be selected since they use a similar algoritm.</help>\n- <option value="X!Tandem" selected="True">X!Tandem</option>\n- <option value="MSGF">MS-GF+</option>\n- <optio'..b'on_string}: proteins">\n@@ -113,12 +133,14 @@\n </actions>\n </data>\n <data format="tabular" name="output_metaproteins" from_work_dir="metaproteins.csv" label="${tool.name} on ${on_string}: metaproteins">\n+ <filter>generate_metaproteins</filter>\n <actions>\n <action name="comment_lines" type="metadata" default="1" />\n <action name="column_names" type="metadata" default="Meta-Protein_Num,Meta-Protein_Accession,Meta-Protein_Description,Meta-Protein_Taxonomy,Meta-Protein_UniRef100,Meta-Protein_UniRef90,Meta-Protein_UniRef50,Meta-Protein_KO,Meta-Protein_EC,Peptide_Count,Spectral_Count,Proteins,Peptides" />\n </actions>\n </data>\n <data format="tabular" name="output_metaprotein_taxa" from_work_dir="metaprotein_taxa.csv" label="${tool.name} on ${on_string}: metaprotein_taxa">\n+ <filter>generate_metaproteins</filter>\n <actions>\n <action name="comment_lines" type="metadata" default="1" />\n <action name="column_names" type="metadata" default="Unclassified,Superkingdom,Kingdom,Phylum,Class,Order,Family,Genus,Species,Subspecies,Num_Peptides,Spectral_Count" />\n@@ -126,7 +148,7 @@\n </data>\n </outputs>\n <tests>\n- <test>\n+ <test expect_num_outputs="6">\n <param name="peak_lists" value="Test416Ebendorf.mgf" ftype="mgf"/>\n <param name="input_database" value="searchdb.fa" ftype="fasta"/>\n <param name="missed_cleavages" value="2"/>\n@@ -134,11 +156,36 @@\n <param name="prec_tol" value="10"/>\n <param name="frag_tol" value="0.5"/>\n <param name="engines" value="X!Tandem,MSGF,Comet"/>\n- <output name="output_PSMs">\n- <assert_contents>\n- <has_text text="A2SPK1" />\n+ <expand macro="test_output" name="output_proteins" has_text="B8GJQ7"/>\n+ <expand macro="test_output" name="output_peptides" has_text="B8GJQ7"/>\n+ <expand macro="test_output" name="output_PSMs" has_text="B8GJQ7">\n+ <assert_contents>\n+ <has_text text="X!Tandem" />\n </assert_contents>\n- </output>\n+ </expand>\n+ <expand macro="test_output" name="output_spectrum_ids" has_text="B8GJQ7"/>\n+ <expand macro="test_output" name="output_metaproteins" has_text="B8GJQ7"/>\n+ <expand macro="test_output" name="output_metaprotein_taxa" has_text="Unknown Superkingdomq"/>\n+ </test>\n+ <test expect_num_outputs="4">\n+ <param name="peak_lists" value="Test416Ebendorf.mgf" ftype="mgf"/>\n+ <param name="input_database" value="searchdb.fa" ftype="fasta"/>\n+ <param name="missed_cleavages" value="2"/>\n+ <param name="prec_tol" value="ppm"/>\n+ <param name="prec_tol" value="10"/>\n+ <param name="frag_tol" value="0.5"/>\n+ <param name="engines" value="MSGF,Comet"/>\n+ <param name="generate_metaproteins" value="0"/>\n+ <expand macro="test_output" name="output_proteins" has_text="B8GJQ7"/>\n+ <expand macro="test_output" name="output_peptides" has_text="B8GJQ7"/>\n+ <expand macro="test_output" name="output_PSMs" has_text="B8GJQ7">\n+ <assert_contents>\n+ <not_has_text text="X!Tandem" />\n+ </assert_contents>\n+ </expand>\n+ <expand macro="test_output" name="output_spectrum_ids" has_text="B8GJQ7"/>\n+ <expand macro="test_output" name="output_metaproteins" has_text="B8GJQ7"/>\n+ <expand macro="test_output" name="output_metaprotein_taxa" has_text="Unknown Superkingdomq"/>\n </test>\n </tests>\n <help>\n@@ -163,10 +210,6 @@\n * spectrum_ids\n * metaproteins\n * metaprotein_taxa\n-\n-\n-------\n-\n </help>\n <citations>\n <citation type="doi">10.1021/pr501246w</citation>\n' |