| Previous changeset 0:3a49065a05d6 (2016-12-07) Next changeset 2:7a0951d0e13e (2017-03-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c |
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modified:
msgf2pin.xml percolator.xml test-data/percolatorOut.txt test-data/percolatorOut.xml test-data/percolatorTab |
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added:
nested_collection.py nested_collection.xml pout2mzid.xml test-data/dataset_2.mzid test-data/percolatorInresult_multifractions.txt test-data/target_ds2_withperco.mzid test-data/target_ds3_withperco.mzid |
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removed:
metafiles2pin.py metafiles2pin.xml test-data/pool0_metafile test-data/pool1_metafile |
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| diff -r 3a49065a05d6 -r 86770eea5b09 metafiles2pin.py --- a/metafiles2pin.py Wed Dec 07 16:43:51 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,54 +0,0 @@ -import argparse -import os -import re -from collections import OrderedDict - - -def get_filename_index_with_identifier(spectrafiles, pool_id): - pool_indices = [] - for index, fn in enumerate(spectrafiles): - if re.search(pool_id, fn) is not None: - pool_indices.append(index) - return pool_indices - - -def get_perco_batches_from_spectrafiles(spectrafiles, batchsize, ppool_ids): - """For an amount of input spectra files, pool identifiers and a batch size, - return batches of files that can be percolated together""" - if ppool_ids: - filegroups = OrderedDict([(p_id, get_filename_index_with_identifier( - spectrafiles, p_id)) for p_id in ppool_ids]) - else: - filegroups = {1: range(len(spectrafiles))} - batch = [] - for grouped_indices in filegroups.values(): - for index in grouped_indices: - batch.append(index) - if len(batch) == int(batchsize): - yield batch - batch = [] - if len(batch) > 0: - yield batch - batch = [] - - -def main(): - parser = argparse.ArgumentParser() - parser.add_argument('--batchsize', dest='batchsize') - parser.add_argument('--spectrafiles', dest='spectrafiles', nargs='+') - parser.add_argument('--searchfiles', dest='searchfiles', nargs='+') - parser.add_argument('--percolator-pool-ids', dest='percopoolids', nargs='+', default=False) - args = parser.parse_args() - outpath = os.path.join(os.getcwd(), 'metafiles') - os.makedirs(outpath) - for count, batch in enumerate(get_perco_batches_from_spectrafiles( - args.spectrafiles, args.batchsize, args.percopoolids)): - batchfiles = [args.searchfiles[index] for index in batch] - out_file = os.path.join(outpath, 'percolatorpool{}.meta2pin'.format( - str(count))) - with open(out_file, 'w') as fp: - fp.write('\n'.join(batchfiles)) - - -if __name__ == '__main__': - main() |
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| diff -r 3a49065a05d6 -r 86770eea5b09 metafiles2pin.xml --- a/metafiles2pin.xml Wed Dec 07 16:43:51 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,116 +0,0 @@ -<tool id="metafiles2pin" name="Merge search data" version="1.0"> - <description>before creating percolator input</description> - <stdio> - <exit_code range="1:" /> - </stdio> - <command>python $__tool_directory__/metafiles2pin.py - --batchsize $percopoolsize - #if len($percopoolids) > 0 - --percolator-pool-ids - #for $ppool in $percopoolids - "${ppool.ppool_identifier}" - #end for - #end if - --spectrafiles - #for $specfile in $searchresult.keys() - "$specfile" - #end for - --searchfiles - #for $specfile in $searchresult.keys() - "$searchresult[$specfile]" - #end for - </command> - <inputs> - <param name="percopoolsize" type="integer" value="8" label="Amount of fractions to batch per Percolator process" /> - <repeat name="percopoolids" title="Percolator pools" help="For cases where file amounts cause search results to not automatically line up into correct percolator batches"> - <param name="ppool_identifier" type="text" label="Filename part identifying percolator pool" - help="Specify part of the input spectra filenames that are unique for each percolator pool, e.g set_A."/> - </repeat> - <param name="searchresult" type="data_collection" format="mzid" label="MSGF+, SQT or XTandem search results" /> - </inputs> - <outputs> - <collection name="metafile_collection" type="list" label="Percolator metafiles list"> - <discover_datasets pattern="__designation_and_ext__" directory="metafiles" /> - </collection> - </outputs> - <tests> - <test> - <param name="percopoolsize" value="2"/> - <param name="searchresult"> - <collection type="list"> - <element name="fraction_one_spectra" value="empty_file1.mzid"/> - <element name="fraction_two_spectra" value="empty_file2.mzid"/> - <element name="fraction_three_spectra" value="empty_file3.mzid"/> - <element name="fraction_four_spectra" value="empty_file4.mzid"/> - </collection> - </param> - <output_collection name="metafile_collection" type="list"> - <element name="percolatorpool0"> - <assert_contents> - <has_text_matching expression="dataset_1.dat" /> - <has_text_matching expression="dataset_2.dat" /> - </assert_contents> - </element> - <element name="percolatorpool1"> - <assert_contents> - <has_text_matching expression="dataset_3.dat" /> - <has_text_matching expression="dataset_4.dat" /> - </assert_contents> - </element> - </output_collection> - </test> - <test> - <param name="percopoolsize" value="2"/> - <repeat name="percopoolids"> - <param name="ppool_identifier" value="set1"/> - </repeat> - <repeat name="percopoolids"> - <param name="ppool_identifier" value="set2"/> - </repeat> - <param name="searchresult"> - <collection type="list"> - <element name="fr_one_set1_spectra" value="empty_file1.mzid"/> - <element name="fr_two_set1_spectra" value="empty_file2.mzid"/> - <element name="fr_three_set1_spectra" value="empty_file3.mzid"/> - <element name="fr_one_set2_spectra" value="empty_file4.mzid"/> - <element name="fr_two_set2_spectra" value="empty_file5.mzid"/> - <element name="fr_three_set2_spectra" value="empty_file6.mzid"/> - </collection> - </param> - <output_collection name="metafile_collection" type="list"> - <element name="percolatorpool0"> - <assert_contents> - <has_text_matching expression="dataset_7.dat" /> - <has_text_matching expression="dataset_8.dat" /> - </assert_contents> - </element> - <element name="percolatorpool1"> - <assert_contents> - <has_text_matching expression="dataset_9.dat" /> - </assert_contents> - </element> - <element name="percolatorpool2"> - <assert_contents> - <has_text_matching expression="dataset_10.dat" /> - <has_text_matching expression="dataset_11.dat" /> - </assert_contents> - </element> - <element name="percolatorpool3"> - <assert_contents> - <has_text_matching expression="dataset_12.dat" /> - </assert_contents> - </element> - </output_collection> - </test> - </tests> - <help> - Creates meta files containing the filenames of the search data in batches of - a specific size. These are used as inputs to sqt2pin, msgfplus2pin or tandem2pin. - Use this feature when you want to batch a specific amount of input search results - to run in percolator, as opposed to one at a time. This tool generates a collection - containing multiple batches of the search results. You can specify batch size as well - as a pattern in the spectra files which makes sure the batching isn't continued through - very different MS sets. Instead, for each filename-pattern it generates batches of the - specified size. - </help> -</tool> |
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| diff -r 3a49065a05d6 -r 86770eea5b09 msgf2pin.xml --- a/msgf2pin.xml Wed Dec 07 16:43:51 2016 -0500 +++ b/msgf2pin.xml Sat Mar 04 20:36:03 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="msgfplus2pin" name="MS-GF+ output to Pin converter" version="3.0"> +<tool id="msgfplus2pin" name="MS-GF+ output to Pin converter" version="3.0.1"> <description>to create Percolator input files</description> <requirements> <requirement type="package" version="3.0">percolator</requirement> @@ -6,17 +6,50 @@ <stdio> <exit_code range="1:"/> </stdio> - <command> - msgf2pin -o $pinout -e $enzyme - #if $matches - -m $matches + <command><![CDATA[ + mkdir target && mkdir decoy && + + #if $mzids.inputtype == "multi" + #for $key in $mzids.target.keys() + ln -s '$mzids.target[$key]' 'target/$key' && + echo 'target/$key' >> targetmeta && + #end for + #for $key in $mzids.decoy.keys() + ln -s '$mzids.decoy[$key]' 'decoy/$key' && + echo 'decoy/$key' >> decoymeta && + #end for + msgf2pin -o $pinout -e $enzyme + #if $matches + -m $matches + #end if + $aafreq $ptm $pngase $isotope targetmeta decoymeta + + #else + ln -s '$mzids.target' 'target/$target.display_name' && + ln -s '$mzids.decoy' 'decoy/$decoy.display_name' && + msgf2pin -o $pinout -e $enzyme + #if $matches + -m $matches + #end if + $aafreq $ptm $pngase $isotope + 'target/$mzids.target.display_name' 'decoy/$mzids.decoy.display_name' #end if - $aafreq $ptm $pngase $isotope - "$target" "$decoy" - </command> + ]]></command> <inputs> - <param name="target" type="data" format="mzid,meta2pin" label="Target MSGF+ results or metafile pointing to them" /> - <param name="decoy" type="data" format="mzid,meta2pin" label="Decoy MSGF+ results or metafile pointing to them" /> + <conditional name="mzids"> + <param name="inputtype" type="select" display="radio"> + <option value="single">Single mzIdentML</option> + <option value="multi">Multiple mzIdentMLs</option> + </param> + <when value="single"> + <param name="target" type="data" format="mzid" label="Target MSGF+ results" /> + <param name="decoy" type="data" format="mzid" label="Decoy MSGF+ results" /> + </when> + <when value="multi"> + <param name="target" type="data_collection" collection_type="list" format="mzid" label="Target MSGF+ results" /> + <param name="decoy" type="data_collection" collection_type="list" format="mzid" label="Decoy MSGF+ results" /> + </when> + </conditional> <param name="enzyme" type="select" label="Enzyme used"> <option value="trypsin">trypsin</option> <option value="no_enzyme">no enzyme</option> @@ -42,22 +75,40 @@ </outputs> <tests> <test> - <param name="target" value="target.mzid"/> - <param name="decoy" value="decoy.mzid"/> + <param name="mzids|inputtype" value="single" /> + <param name="mzids|target" value="target.mzid" /> + <param name="mzids|decoy" value="decoy.mzid" /> <param name="ptm" value="true"/> <param name="matches" value="1"/> <output name="pinout" value="percolatorInresult.txt" compare="sim_size" delta="20" /> </test> + <test> + <param name="mzids|inputtype" value="multi" /> + <param name="mzids|target"> + <collection type="list"> + <element name="target1" value="target.mzid" /> + <element name="target2" value="target.mzid" /> + </collection> + </param> + <param name="mzids|decoy"> + <collection type="list"> + <element name="decoy1" value="decoy.mzid" /> + <element name="decoy2" value="decoy.mzid" /> + </collection> + </param> + <param name="ptm" value="true"/> + <param name="matches" value="1"/> + <output name="pinout" value="percolatorInresult_multifractions.txt" compare="sim_size" delta="20" /> + </test> </tests> <help> The percolator converter msgf2pin converts mzIdentML to input for percolator. Target and decoy inputs are MzIdentML-files of MS-GF+ from separate target and decoy searches. Internal MS-GF+ target/decoy analysis should be turned off, and the addFeatures options turned on. -Multiple MzIdentML-files can be merged by replacing target and decoy -filepaths with meta files. Meta files are text files containing the -the paths of mzid-files, one path per line. For successful results, -the different runs should be generated under similar conditions. +Multiple MzIdentML-files can be merged by passing lists of these. +For successful results, the different runs should be generated under +similar conditions. </help> <citations> <citation type="doi">10.1021/pr400937n</citation> |
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| diff -r 3a49065a05d6 -r 86770eea5b09 nested_collection.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nested_collection.py Sat Mar 04 20:36:03 2017 -0500 |
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| @@ -0,0 +1,52 @@ +import argparse +import os +import re +from collections import OrderedDict + + +def get_filename_index_with_identifier(realnames, pool_id): + pool_indices = [] + for index, fn in enumerate(realnames): + if re.search(pool_id, fn) is not None: + pool_indices.append(index) + return pool_indices + + +def get_batches_of_galaxyfiles(realnames, batchsize, pool_ids): + """For an amount of input files, pool identifiers and a batch size, + return batches of files for a list of lists""" + if pool_ids: + filegroups = OrderedDict([(p_id, get_filename_index_with_identifier( + realnames, p_id)) for p_id in pool_ids]) + else: + filegroups = {1: range(len(realnames))} + batch = [] + for pool_id, grouped_indices in filegroups.items(): + if pool_id == 1: + pool_id = 'pool0' + for index in grouped_indices: + batch.append(index) + if batchsize and len(batch) == int(batchsize): + yield pool_id, batch + batch = [] + if len(batch) > 0: + yield pool_id, batch + batch = [] + + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument('--batchsize', dest='batchsize', default=False) + parser.add_argument('--real-names', dest='realnames', nargs='+') + parser.add_argument('--galaxy-files', dest='galaxyfiles', nargs='+') + parser.add_argument('--pool-ids', dest='poolids', nargs='+', default=False) + args = parser.parse_args() + for batchcount, (pool_id, batch) in enumerate(get_batches_of_galaxyfiles( + args.realnames, args.batchsize, args.poolids)): + for fncount, batchfile in enumerate([args.galaxyfiles[index] for index in batch]): + dsetname = '{}___batch{}_inputfn{}.mzid'.format(pool_id, batchcount, fncount) + print('producing', dsetname) + os.symlink(batchfile, dsetname) + +if __name__ == '__main__': + main() |
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| diff -r 3a49065a05d6 -r 86770eea5b09 nested_collection.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nested_collection.xml Sat Mar 04 20:36:03 2017 -0500 |
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| @@ -0,0 +1,137 @@ +<tool id="batched_set_list_creator" name="Create nested list" version="3.0.1"> + <description>based on filenames and batch sizes</description> + <stdio> + <exit_code range="1:" /> + </stdio> + <command>python $__tool_directory__/nested_collection.py + #if $batchsize + --batchsize $batchsize + #end if + #if len($poolids) > 0 + --pool-ids + #for $pool in $poolids + '${pool.pool_identifier}' + #end for + #end if + --real-names + #for $fname in $listtobatch.keys() + '$fname' + #end for + --galaxy-files + #for $fname in $listtobatch.keys() + '$listtobatch[$fname]' + #end for + </command> + <inputs> + <param name="batchsize" type="integer" optional="true" value="" label="Maximal amount of fractions to batch." help="No value means no maximum" /> + <repeat name="poolids" title="Batch pools" help="Pools containing batches (optional, not using this will result in one pool)"> + <param name="pool_identifier" type="text" label="Filename part identifying batchpool" + help="Specify part of the input filenames that are unique for each pool, e.g set_A. Do not use 3 consecutive underscores."/> + </repeat> + <param name="listtobatch" type="data_collection" collection_type="list" label="List of files to batch" /> + </inputs> + <outputs> + <collection name="batched_fractions" type="list:list" label="Pooled batched data"> + <discover_datasets pattern="[a-zA-z0-9_]*___(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.mzid" ext="mzid" visible="true" /> + </collection> + </outputs> + <tests> + <test> + <param name="batchsize" value="2"/> + <param name="listtobatch"> + <collection type="list"> + <element name="fraction_one_spectra" value="empty_file1.mzid"/> + <element name="fraction_two_spectra" value="empty_file2.mzid"/> + <element name="fraction_three_spectra" value="empty_file3.mzid"/> + <element name="fraction_four_spectra" value="empty_file4.mzid"/> + </collection> + </param> + <output_collection name="batched_fractions" type="list:list"> + <element name="batch0"> + <element name="inputfn0" file="empty_file1.mzid"/> + <element name="inputfn1" file="empty_file2.mzid"/> + </element> + <element name="batch1"> + <element name="inputfn0" file="empty_file3.mzid"/> + <element name="inputfn1" file="empty_file4.mzid"/> + </element> + </output_collection> + </test> + <test> + <repeat name="poolids"> + <param name="pool_identifier" value="set1"/> + </repeat> + <repeat name="poolids"> + <param name="pool_identifier" value="set2"/> + </repeat> + <param name="listtobatch"> + <collection type="list"> + <element name="fr_one_set1_spectra" value="empty_file1.mzid"/> + <element name="fr_two_set1_spectra" value="empty_file2.mzid"/> + <element name="fr_three_set1_spectra" value="empty_file3.mzid"/> + <element name="fr_one_set2_spectra" value="empty_file4.mzid"/> + <element name="fr_two_set2_spectra" value="empty_file5.mzid"/> + <element name="fr_three_set2_spectra" value="empty_file6.mzid"/> + </collection> + </param> + <output_collection name="batched_fractions" type="list:list"> + <element name="batch0"> + <element name="inputfn0" file="empty_file1.mzid"/> + <element name="inputfn1" file="empty_file2.mzid"/> + <element name="inputfn2" file="empty_file3.mzid"/> + </element> + <element name="batch1"> + <element name="inputfn0" file="empty_file4.mzid"/> + <element name="inputfn1" file="empty_file5.mzid"/> + <element name="inputfn2" file="empty_file6.mzid"/> + </element> + </output_collection> + </test> + <test> + <param name="batchsize" value="2"/> + <repeat name="poolids"> + <param name="pool_identifier" value="set1"/> + </repeat> + <repeat name="poolids"> + <param name="pool_identifier" value="set2"/> + </repeat> + <param name="listtobatch"> + <collection type="list"> + <element name="fr_one_set1_spectra" value="empty_file1.mzid"/> + <element name="fr_two_set1_spectra" value="empty_file2.mzid"/> + <element name="fr_three_set1_spectra" value="empty_file3.mzid"/> + <element name="fr_one_set2_spectra" value="empty_file4.mzid"/> + <element name="fr_two_set2_spectra" value="empty_file5.mzid"/> + <element name="fr_three_set2_spectra" value="empty_file6.mzid"/> + </collection> + </param> + <output_collection name="batched_fractions" type="list:list"> + <element name="batch0"> + <element name="inputfn0" file="empty_file1.mzid"/> + <element name="inputfn1" file="empty_file2.mzid"/> + </element> + <element name="batch1"> + <element name="inputfn0" file="empty_file3.mzid"/> + </element> + <element name="batch2"> + <element name="inputfn0" file="empty_file4.mzid"/> + <element name="inputfn1" file="empty_file5.mzid"/> + </element> + <element name="batch3"> + <element name="inputfn0" file="empty_file6.mzid"/> + </element> + </output_collection> + </test> + </tests> + <help> + Creates nested collection containing from a list containing datasets in batches of + a specific size. Useful when e.g. creating inputs to sqt2pin, msgfplus2pin or tandem2pin. + Use this feature when you want to batch a specific amount of datasets, or datasets with + a common file name pattern, or both. + The tool generates a collection containing batches which contain multiple batches + of input files. The pools are specified as a pattern in the input + files which makes sure the batching isn't continued through very different input sets + if that is a problem. Instead, for each filename-pattern it generates batches of the + specified size. + </help> +</tool> |
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| diff -r 3a49065a05d6 -r 86770eea5b09 percolator.xml --- a/percolator.xml Wed Dec 07 16:43:51 2016 -0500 +++ b/percolator.xml Sat Mar 04 20:36:03 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="percolator" name="Percolator" version="3.0"> +<tool id="percolator" name="Percolator" version="3.0.1"> <description>accurate peptide identification</description> <requirements> <requirement type="package" version="3.0">percolator</requirement> @@ -39,7 +39,7 @@ <inputs> <param name="output_type" label="What filetype to output" type="select" display="radio"> <option value="xml" selected="true">percolator XML (for further processing)</option> - <option value="tsv">Tab-separated</option> + <option value="tsv">Tab-separated</option> </param> <param name="input" type="data" format="percin" label="Percolator input data" /> <param name="cpos" label="Penalty for mistakes on positive examples" type="float" optional="true" /> |
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| diff -r 3a49065a05d6 -r 86770eea5b09 pout2mzid.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pout2mzid.xml Sat Mar 04 20:36:03 2017 -0500 |
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| @@ -0,0 +1,94 @@ +<tool id="pout2mzid" name="Pout2mzid" version="0.3.03"> + <description>add Percolator scoring to mzIdentML</description> + <requirements> + <requirement type="package" version="0.3.03">pout2mzid</requirement> + </requirements> + <stdio> + <exit_code range="1:"/> + </stdio> + <command><![CDATA[ + #if $mzid.multifile == "true" + mkdir p2m_mzid_in && + #set digits = "0" + str(len(str(len($mzid.mzids.keys())))) + #for $i, $fn in $enumerate($mzid.mzids.keys()) + #set prefixnum = format($i, $digits) + ln -s '$mzid.mzids[$fn]' 'p2m_mzid_in/$fn' && + #end for + ls p2m_mzid_in > infiles.txt && + pout2mzid -p '$percout' -i p2m_mzid_in -f infiles.txt -o p2m_result -c _perco + + #else + ln -s '$mzid.mzidsingle' '$mzid.mzidsingle.display_name' && + pout2mzid -p '$percout' -m '$mzid.mzidsingle.display_name' + #end if + + #if $targetdecoy == "decoy" + -d + #end if + #if $schemaskip + -v + #end if + #if $mzid.multifile == "false" + > '$output_single' + #end if + ]]></command> + <inputs> + <param name="percout" type="data" format="percout" label="Percolator output"/> + <conditional name="mzid"> + <param name="multifile" type="select" display="radio" label="Multiple mzIdentML files?"> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <when value="true"> + <param name="mzids" type="data_collection" collection_type="list" format="mzid" label="mzIdentML from MSGF+" /> + </when> + <when value="false"> + <param name="mzidsingle" type="data" format="mzid" label="mzIdentML from MSGF+" /> + </when> + </conditional> + <param name="targetdecoy" type="select" display="radio" label="Which features to add to mzIdentML"> + <option value="target" selected="true">Target</option> + <option value="decoy">Decoy</option> + </param> + <param name="schemaskip" type="boolean" label="Skip percolator schema validation?" /> + </inputs> + <outputs> + <data name="output_single" format="mzid"> + <filter>mzid['multifile'] == "false"</filter> + </data> + <collection name="output_multi" type="list"> + <filter>mzid['multifile'] == "true"</filter> + <discover_datasets pattern="__designation__" ext="mzid" directory="p2m_result" /> + </collection> + + </outputs> + <tests> + <test> + <param name="percout" value="percolatorOut.xml" /> + <param name="mzid|multifile" value="false" /> + <param name="mzid|mzidsingle" value="dataset_2.mzid" /> + <param name="targetdecoy" value="target" /> + <param name="schemaskip" value="true" /> + <output name="output_single" value="target_ds2_withperco.mzid" /> + </test> + <test> + <param name="percout" value="percolatorOut.xml" /> + <param name="mzid|multifile" value="true" /> + <param name="mzid|mzids"> + <collection type="list"> + <element name="dataset_2.mzid" value="dataset_2.mzid" /> + <element name="dataset_3.mzid" value="dataset_2.mzid" /> + </collection> + </param> + <param name="targetdecoy" value="target" /> + <param name="schemaskip" value="true" /> + <output_collection name="output_multi" type="list"> + <element name="dataset_2_perco.mzid" value="target_ds2_withperco.mzid" /> + <element name="dataset_3_perco.mzid" value="target_ds3_withperco.mzid" /> + </output_collection> + </test> + </tests> + <help>Pout2Mzid extracts statistics from a percolator input file, and writes them to the mzIdentML file(s) that have been used + to generate the percolator data. You may either pass multiple mzIdentML files in a list and one percolator file, or a single one. + </help> +</tool> |
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| diff -r 3a49065a05d6 -r 86770eea5b09 test-data/dataset_2.mzid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_2.mzid Sat Mar 04 20:36:03 2017 -0500 |
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| b'@@ -0,0 +1,381 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<MzIdentML id="MS-GF+" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2017-03-01T15:00:34" >\n+<cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">\n+ <cv id="PSI-MS" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.30.0" fullName="PSI-MS"/>\n+ <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/>\n+ <cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" fullName="UNIT-ONTOLOGY"/>\n+</cvList>\n+<AnalysisSoftwareList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">\n+ <AnalysisSoftware version="Beta (v10072)" name="MS-GF+" id="ID_software">\n+ <SoftwareName>\n+ <cvParam 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</SearchModification>\n+ <SearchModification residues="K" massDelta="229.16293" fixedMod="true">\n+ <cvParam accession="UNIMOD:737" cvRef="UNIMOD" name="TMT6plex"/>\n+ </SearchModification>\n+ <SearchModification residues="." massDelta="229.16293" fixedMod="true">\n+ <SpecificityRules>\n+ <cvParam accession="MS:1001189" cvRef="PSI-MS" name="modification specificity N-term"/>\n+ </SpecificityRules>\n+ <cvParam accession="UNIMOD:737" cvRef="UNIMOD" name="TMT6plex"/>\n+ </SearchModification>\n+ </ModificationParams>\n+ <Enzymes>\n+ <Enzyme missedCleavages="1000" semiSpecific="false" id="Tryp">\n+ <Enzym'..b'SpecEValue"/>\n+ <cvParam accession="MS:1002053" cvRef="PSI-MS" value="238630.45" name="MS-GF:EValue"/>\n+ <userParam value="0" name="IsotopeError"/>\n+ <userParam value="HCD" name="AssumedDissociationMethod"/>\n+ <userParam value="0.030569095" name="ExplainedIonCurrentRatio"/>\n+ <userParam value="0.00203066" name="NTermIonCurrentRatio"/>\n+ <userParam value="0.028538436" name="CTermIonCurrentRatio"/>\n+ <userParam value="1176358.8" name="MS2IonCurrent"/>\n+ <userParam value="4" name="NumMatchedMainIons"/>\n+ <userParam value="7.255852" name="MeanErrorAll"/>\n+ <userParam value="3.8946548" name="StdevErrorAll"/>\n+ <userParam value="7.255852" name="MeanErrorTop7"/>\n+ <userParam value="3.8946548" name="StdevErrorTop7"/>\n+ <userParam value="-2.0970254" name="MeanRelErrorAll"/>\n+ <userParam value="7.9635553" name="StdevRelErrorAll"/>\n+ <userParam value="-2.0970254" name="MeanRelErrorTop7"/>\n+ <userParam value="7.9635553" name="StdevRelErrorTop7"/>\n+ </SpectrumIdentificationItem>\n+ <cvParam accession="MS:1001115" cvRef="PSI-MS" value="9594" name="scan number(s)"/>\n+ </SpectrumIdentificationResult>\n+ <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=9681" id="SIR_182">\n+ <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep371" calculatedMassToCharge="388.7393798828125" experimentalMassToCharge="389.2425537109375" chargeState="2" id="SII_182_1">\n+ <PeptideEvidenceRef peptideEvidence_ref="PepEv_8122661_371_164"/>\n+ <PeptideEvidenceRef peptideEvidence_ref="PepEv_8122856_371_29"/>\n+ <PeptideEvidenceRef peptideEvidence_ref="PepEv_8123174_371_89"/>\n+ <PeptideEvidenceRef peptideEvidence_ref="PepEv_8123331_371_113"/>\n+ <cvParam accession="MS:1002049" cvRef="PSI-MS" value="-63" name="MS-GF:RawScore"/>\n+ <cvParam accession="MS:1002050" cvRef="PSI-MS" value="12" name="MS-GF:DeNovoScore"/>\n+ <cvParam accession="MS:1002052" cvRef="PSI-MS" value="0.041115593" name="MS-GF:SpecEValue"/>\n+ <cvParam accession="MS:1002053" cvRef="PSI-MS" value="460070.12" name="MS-GF:EValue"/>\n+ <userParam value="1" name="IsotopeError"/>\n+ <userParam value="HCD" name="AssumedDissociationMethod"/>\n+ <userParam value="0.0032015902" name="ExplainedIonCurrentRatio"/>\n+ <userParam value="6.9299503E-4" name="NTermIonCurrentRatio"/>\n+ <userParam value="0.0025085951" name="CTermIonCurrentRatio"/>\n+ <userParam value="1018012.9" name="MS2IonCurrent"/>\n+ <userParam value="3" name="NumMatchedMainIons"/>\n+ <userParam value="9.696182" name="MeanErrorAll"/>\n+ <userParam value="1.2990792" name="StdevErrorAll"/>\n+ <userParam value="9.696182" name="MeanErrorTop7"/>\n+ <userParam value="1.2990792" name="StdevErrorTop7"/>\n+ <userParam value="-9.696182" name="MeanRelErrorAll"/>\n+ <userParam value="1.2990792" name="StdevRelErrorAll"/>\n+ <userParam value="-9.696182" name="MeanRelErrorTop7"/>\n+ <userParam value="1.2990792" name="StdevRelErrorTop7"/>\n+ </SpectrumIdentificationItem>\n+ <cvParam accession="MS:1001115" cvRef="PSI-MS" value="9681" name="scan number(s)"/>\n+ </SpectrumIdentificationResult>\n+ </SpectrumIdentificationList>\n+ </AnalysisData>\n+</DataCollection>\n+</MzIdentML>\n' |
| b |
| diff -r 3a49065a05d6 -r 86770eea5b09 test-data/percolatorInresult_multifractions.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/percolatorInresult_multifractions.txt Sat Mar 04 20:36:03 2017 -0500 |
| [ |
| @@ -0,0 +1,4 @@ +SpecId Label ScanNr ExpMass CalcMass RawScore DeNovoScore ScoreRatio Energy lnEValue IsotopeError lnExplainedIonCurrentRatio lnNTermIonCurrentRatio lnCTermIonCurrentRatio lnMS2IonCurrent Mass PepLen dM absdM MeanErrorTop7 sqMeanErrorTop7 StdevErrorTop7 Charge2 Charge3 Charge4 Charge5 enzN enzC enzInt ptm Peptide Proteins +DefaultDirection - - - - 0 -1 0 -2 6 -2.5 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 +decoy_SII_80_1_180_3_1 -1 180 1501.37 1501.04 -131 22 -1 153 -9.16055 1 -3.23882 -9.21034 -3.23882 10.4876 1501.37 33 -2.96829e-06 2.96829e-06 28.587 51.0759 28.587 0 1 0 0 1 1 2 5 K.[UNIMOD:737]LRPAFRQC[UNIMOD:4]C[UNIMOD:4]YELHAGELGWYIMENYFSLEC[UNIMOD:4]M[UNIMOD:35]RR.D decoy_ENSP00000304127 decoy_ENSP00000378424 +decoy_SII_80_1_180_3_1 -1 180 1501.37 1501.04 -131 22 -1 153 -9.16055 1 -3.23882 -9.21034 -3.23882 10.4876 1501.37 33 -2.96829e-06 2.96829e-06 28.587 51.0759 28.587 0 1 0 0 1 1 2 5 K.[UNIMOD:737]LRPAFRQC[UNIMOD:4]C[UNIMOD:4]YELHAGELGWYIMENYFSLEC[UNIMOD:4]M[UNIMOD:35]RR.D decoy_ENSP00000304127 decoy_ENSP00000378424 |
| b |
| diff -r 3a49065a05d6 -r 86770eea5b09 test-data/percolatorOut.txt --- a/test-data/percolatorOut.txt Wed Dec 07 16:43:51 2016 -0500 +++ b/test-data/percolatorOut.txt Sat Mar 04 20:36:03 2017 -0500 |
| [ |
| b'@@ -1,7686 +1,2103 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1\t0.570572\t-0.44017\t-0.206591\t-0.157728\t-0.135719\t0.156136\t0.215209\t0.0778837\tR.[UNIMOD:737]NC[UNIMOD:4]HEGK[UNIMOD:737]K[UNIMOD:737].S\tdecoy_ENSP00000484039.1\n+dataset_88023_SII_10535_1_10535_2_1\t-1\t10535\t1209.14\t1209.64\t0.105083\t0.736987\t0.190286\t0.743007\t0.300923\t-1.21582\t0.332473\t-0.246548\t0.766653\t0.216179\t1.85797\t0.734038\t0.136351\t-1.59751\t-1.67589\t1.51103\t-1.86709\t0.570572\t-0.44017\t-0.206591\t-0.157728\t-0.135719\t0.156136\t0.215209\t0.0778837\tK.[UNIMOD:737]K[UNIMOD:737]QVEC[UNIMOD:4]NQSTAGYSMK[UNIMOD:737].K\tdecoy_ENSP00000316909.4\tdecoy_ENSP00000376715.3\n+dataset_88023_SII_10536_1_10536_2_1\t-1\t10536\t699.383\t699.386\t-0.39273\t-0.792149\t0.190189\t-0.62163\t0.0993306\t-0.293973\t-1.00695\t-1.42201\t-0.182754\t0.31847\t0.0319527\t-0.586633\t-0.604415\t-0.160623\t-1.61704\t1.39427\t-1.81372\t0.570572\t-0.44017\t-0.206591\t-0.157728\t-0.135719\t-6.40469\t0.215209\t-0.441588\tR.[UNIMOD:737]PPC[UNIMOD:4]QFYK[UNIMOD:737].H\tdecoy_ENSP00000355151.5\tdecoy_ENSP00000378500.1\tdecoy_ENSP00000223398.6\n+dataset_88023_SII_10537_1_10537_2_1\t-1\t10537\t995.5\t995.008\t-0.807574\t-0.808077\t0.190106\t-0.376695\t0.0263529\t0.627874\t-0.346274\t-1.42201\t0.300419\t-0.7993\t1.09268\t0.0737024\t-1.47326\t1.5247\t-1.14442\t0.57119\t-1.3851\t0.570572\t-0.44017\t-0.206591\t-0.157728\t-0.135719\t0.156136\t0.215209\t0.597356\tR.[UNIMOD:737]K[UNIMOD:737]REYEDMFC[UNIMOD:4]PR.V\tdecoy_ENSP00000460850.1\tdecoy_ENSP00000458886.1\tdecoy_ENSP00000344392.5\tdecoy_ENSP00000460706.1\tdecoy_ENSP00000460889.1\tdecoy_ENSP00000458513.1\n+dataset_88023_SII_10540_1_10540_2_1\t-1\t10540\t1471.35\t1471.34\t0.160396\t1.45377\t0.190287\t1.49531\t0.850846\t-0.293973\t1.74829\t1.66722\t0.836963\t-0.764271\t2.79723\t1.72454\t1.57821\t0.988901\t0.358962\t-0.541972\t0.158175\t0.570572\t-0.44017\t-0.206591\t-0.157728\t-0.135719\t0.156136\t0.215209\t2.15577\tR.[UNIMOD:737]TAILDGSEPDIRRDLRERRSK[UNIMOD:737].V\tdecoy_ENSP00000377862.3\tdecoy_ENSP00000335169.5\n+dataset_88023_SII_10541_1_10541_3_1\t-1\t10541\t981.236\t980.562\t0.215709\t1.61305\t0.190287\t1.63527\t0.466189\t1.54972\t0.399969\t-1.42201\t0.846167\t-0.0237795\t1.04158\t0.899122\t1.15814\t0.17409\t-1.5729\t1.30879\t-1.77369\t-1.75263\t2.27185\t-0.206591\t-0.157728\t-0.135719\t0.156136\t0.215209\t1.11683\tK.[UNIMOD:737]K[UNIMOD:737]RAESIRPFMNEC[UNIMOD:4]EK[UNIMOD:737]K[UNIMOD:737].C\tdecoy_ENSP00000348086.6\tdecoy_ENSP00000445093.1\n+dataset_88023_SII_10670_1_10670_2_1\t-1\t10670\t952.558\t953.052\t-0.39273\t-0.871791\t-4.7669\t-0.709107\t0.449227\t-1.21582\t-0.486914\t-1.42201\t0.197565\t-1.78237\t0.938857\t0.0737024\t1.51226\t0.860976\t0.502306\t-0.707205\t0.108284\t0.570572\t-0.44017\t-0.206591\t-0.157728\t-0.135719\t0.156136\t0.215209\t0.0778837\tK.[UNIMOD:737]FMIK[UNIMOD:737]HM[UNIMOD:35]QLLNR.L\tdecoy_ENSP00000386088.2\tdecoy_ENSP00000385995.4\tdecoy_ENSP00000385441.2\tdecoy_ENSP00000384266.1\tdecoy_ENSP00000385469.1\n+dataset_88023_SII_10750_1_10750_2_1\t-1\t10750\t983.037\t983.543\t-0.752262\t-0.680649\t0.19023\t-0.271723\t0.179849\t-1.21582\t-0.159607\t-1.42201\t0.436934\t-1.46467\t1.04804\t-0.256466\t-0.60674\t-0.156114\t1.5679\t0.393583\t0.627732\t0.570572\t-0.44017\t-0.206591\t-0.157728\t-0.135719\t0.156136\t-4.64665\t0.597356\tK.[UNIMOD:737]DK[UNIMOD:737]WQEK[UNIMOD:737]C[UNIMOD:4]ER.P\tdecoy_ENSP00000379524.2\n+dataset_88023_SII_10766_1_10766_2_1\t-1\t10766\t806.934\t807.44\t-0.0608544\t-0.537293\t0.190273\t-0.551649\t0.707018\t-1.21582\t0.481927\t0.931831\t-0.229674\t-0.824195\t0.417214\t-0.0913816\t-0.682976\t-0.00823587\t0.563801\t-0.705657\t0.718356\t0.570572\t-0.44017\t-0.206591\t-0.157728\t-0.135719\t0.156136\t0.215209\t-0.441588\tR.[UNIMOD:737]TFTNLC[UNIMOD:4]SGQK[UNIMOD:737].S\tdecoy_ENSP00000357027.3\n' |
| b |
| diff -r 3a49065a05d6 -r 86770eea5b09 test-data/percolatorOut.xml --- a/test-data/percolatorOut.xml Wed Dec 07 16:43:51 2016 -0500 +++ b/test-data/percolatorOut.xml Sat Mar 04 20:36:03 2017 -0500 |
| [ |
| b'@@ -7,82726 +7,43762 @@\n p:majorVersion="3" p:minorVersion="00" p:percolator_version="Percolator version 3.00">\n \n <process_info>\n- <command_line>percolator -j tools/percolator/test-data/percolatorTab -X tools/percolator/test-data/percolatorOut2.xml --decoy-xml-output</command_line>\n+ <command_line>percolator -j testpin -X percolator30Out.xml --decoy-xml-output</command_line>\n <other_command_line></other_command_line>\n <pi_0_psms>1</pi_0_psms>\n <pi_0_peptides>1</pi_0_peptides>\n- <psms_qlevel>260</psms_qlevel>\n- <peptides_qlevel>196</peptides_qlevel>\n+ <psms_qlevel>60</psms_qlevel>\n+ <peptides_qlevel>60</peptides_qlevel>\n </process_info>\n \n <psms>\n- <psm p:psm_id="trg_3902_3_1" p:decoy="false">\n- <svm_score>1.247111</svm_score>\n+ <psm p:psm_id="dataset_2_SII_259_1_9758_3_1" p:decoy="false">\n+ <svm_score>2.813409</svm_score>\n <q_value>0.000000e+00</q_value>\n- <pep>2.466573e-04</pep>\n- <exp_mass>1745.8100</exp_mass>\n- <calc_mass>1745.810</calc_mass>\n- <peptide_seq n="K" c="D" seq="GKDNAEGQGESLADQAR"/>\n- <protein_id>tr|A7A224|A7A224_YEAS7</protein_id>\n- <p_value>5.921e-04</p_value>\n- </psm>\n- <psm p:psm_id="trg_4138_2_1" p:decoy="false">\n- <svm_score>1.206</svm_score>\n- <q_value>0.000e+00</q_value>\n- <pep>3.010e-04</pep>\n- <exp_mass>1676.8700</exp_mass>\n- <calc_mass>1676.860</calc_mass>\n- <peptide_seq n="K" c="Y" seq="GATYGKPTNQGVNELK"/>\n- <protein_id>tr|A6ZMI1|A6ZMI1_YEAS7</protein_id>\n- <protein_id>tr|A7A0T5|A7A0T5_YEAS7</protein_id>\n- <p_value>5.921e-04</p_value>\n- </psm>\n- <psm p:psm_id="trg_2599_3_1" p:decoy="false">\n- <svm_score>1.113</svm_score>\n- <q_value>0.000e+00</q_value>\n- <pep>4.748e-04</pep>\n- <exp_mass>2591.1500</exp_mass>\n- <calc_mass>2591.140</calc_mass>\n- <peptide_seq n="R" c="-" seq="QQQQQQDQPEQSEQPEQHQDK"/>\n- <protein_id>tr|A6ZTA7|A6ZTA7_YEAS7</protein_id>\n- <p_value>5.921e-04</p_value>\n- </psm>\n- <psm p:psm_id="trg_4303_2_1" p:decoy="false">\n- <svm_score>1.109</svm_score>\n- <q_value>0.000e+00</q_value>\n- <pep>4.848e-04</pep>\n- <exp_mass>1627.8400</exp_mass>\n- <calc_mass>1627.830</calc_mass>\n- <peptide_seq n="K" c="I" seq="VEEQEQQQQQIIK"/>\n- <protein_id>tr|A6ZSN7|A6ZSN7_YEAS7</protein_id>\n- <p_value>5.921e-04</p_value>\n- </psm>\n- <psm p:psm_id="trg_4070_2_1" p:decoy="false">\n- <svm_score>1.029</svm_score>\n- <q_value>0.000e+00</q_value>\n- <pep>7.172e-04</pep>\n- <exp_mass>1884.9800</exp_mass>\n- <calc_mass>1884.970</calc_mass>\n- <peptide_seq n="K" c="I" seq="EKVEEQEQQQQQIIK"/>\n- <protein_id>tr|A6ZSN7|A6ZSN7_YEAS7</protein_id>\n- <p_value>5.921e-04</p_value>\n- </psm>\n- <psm p:psm_id="trg_3693_3_1" p:decoy="false">\n- <svm_score>1.002</svm_score>\n- <q_value>0.000e+00</q_value>\n- <pep>8.160e-04</pep>\n- <exp_mass>1759.8700</exp_mass>\n- <calc_mass>1759.860</calc_mass>\n- <peptide_seq n="K" c="A" seq="WTNKDTDAEGKPLER"/>\n- <protein_id>tr|A6ZNY0|A6ZNY0_YEAS7</protein_id>\n- <p_value>5.921e-04</p_value>\n- </psm>\n- <psm p:psm_id="trg_3870_2_1" p:decoy="false">\n- <svm_score>0.965</svm_score>\n- <q_value>0.000e+00</q_value>\n- <pep>9.776e-04</pep>\n- <exp_mass>1638.7400</exp_mass>\n- <calc_mass>1638.730</calc_mass>\n- <peptide_seq n="R" c="T" seq="VGKGDDEANGATSFDR"/>\n- <protein_id>tr|A6ZNR5|A6ZNR5_YEAS7</protein_id>\n- <p_value>5.921e-04</p_value>\n- </psm>\n- <psm p:psm_id="trg_3890_3_1" p:decoy="false">\n- <svm_score>0.961</svm_score>\n- <q_value>0.000e+00</q_value>\n- <pep>9.979e-04</pep>\n- <exp_mass>1638.7400</exp_mass>\n- <calc_mass>1638.730</calc_mass>\n- <peptide_seq n="R" c="T" seq="VGKGDDEANGATSFDR"/>\n- <protein_id>tr|A6ZNR5|A6ZNR5_YEAS7</protein_id>\n- <p_value>5.921e-04</p_value>\n- </psm>\n- <psm p:psm_id="trg_4186_3_1"'..b'id="[UNIMOD:737]M[UNIMOD:35]TM[UNIMOD:35]RGGPC[UNIMOD:4]HK[UNIMOD:737]RPTK[UNIMOD:737]AK[UNIMOD:737]EK[UNIMOD:737]RNK[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]RK[UNIMOD:737]EILR" p:decoy="true">\n+ <svm_score>-2.304</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>1003.3000</exp_mass>\n+ <calc_mass>1003.300</calc_mass>\n+ <protein_id>decoy_ENSP00000428940.1</protein_id>\n+ <protein_id>decoy_ENSP00000427937.1</protein_id>\n+ <protein_id>decoy_ENSP00000276659.5</protein_id>\n+ <protein_id>decoy_ENSP00000428614.1</protein_id>\n+ <p_value>9.978e-01</p_value>\n+ <psm_ids>\n+ <psm_id>dataset_88023_SII_10224_1_10224_6_1</psm_id>\n+ </psm_ids>\n+ </peptide>\n+ <peptide p:peptide_id="[UNIMOD:737]QREK[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]ELERWLEEK[UNIMOD:737]K[UNIMOD:737]LEELK[UNIMOD:737]LK[UNIMOD:737]K[UNIMOD:737]ELAK[UNIMOD:737]" p:decoy="true">\n+ <svm_score>-2.508</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>979.6190</exp_mass>\n+ <calc_mass>979.460</calc_mass>\n+ <protein_id>decoy_ENSP00000261461.2</protein_id>\n+ <protein_id>decoy_ENSP00000442866.1</protein_id>\n+ <p_value>9.985e-01</p_value>\n+ <psm_ids>\n+ <psm_id>dataset_88023_SII_10081_1_10081_6_1</psm_id>\n+ </psm_ids>\n+ </peptide>\n+ <peptide p:peptide_id="[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]RK[UNIMOD:737]HK[UNIMOD:737]K[UNIMOD:737]EK[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]DK[UNIMOD:737]" p:decoy="true">\n+ <svm_score>-2.583</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>846.0940</exp_mass>\n+ <calc_mass>846.257</calc_mass>\n+ <protein_id>decoy_ENSP00000272139.4</protein_id>\n+ <p_value>9.993e-01</p_value>\n+ <psm_ids>\n+ <psm_id>dataset_88023_SII_10136_1_10136_6_1</psm_id>\n+ </psm_ids>\n+ </peptide>\n+ <peptide p:peptide_id="[UNIMOD:737]TK[UNIMOD:737]K[UNIMOD:737]ERK[UNIMOD:737]EEM[UNIMOD:35]TSEK[UNIMOD:737]K[UNIMOD:737]EVTLEK[UNIMOD:737]K[UNIMOD:737]RPTREEM[UNIMOD:35]RK[UNIMOD:737]EVILEK[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]RK[UNIMOD:737]ETSEK[UNIMOD:737]TK[UNIMOD:737]" p:decoy="true">\n+ <svm_score>-2.593</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>1548.7900</exp_mass>\n+ <calc_mass>1548.780</calc_mass>\n+ <protein_id>decoy_ENSP00000362455.3</protein_id>\n <p_value>1.000e+00</p_value>\n <psm_ids>\n- <psm_id>dec_3448_2_1</psm_id>\n- </psm_ids>\n- </peptide>\n- <peptide p:peptide_id="SCSSSC" p:decoy="false">\n- <svm_score>-2.101</svm_score>\n- <q_value>8.250e-01</q_value>\n- <pep>1.000e+00</pep>\n- <exp_mass>687.2040</exp_mass>\n- <calc_mass>687.207</calc_mass>\n- <protein_id>tr|A6ZNS1|A6ZNS1_YEAS7</protein_id>\n- <p_value>1.000e+00</p_value>\n- <psm_ids>\n- <psm_id>trg_712_1_1</psm_id>\n- </psm_ids>\n- </peptide>\n- <peptide p:peptide_id="MDDMDD" p:decoy="false">\n- <svm_score>-2.106</svm_score>\n- <q_value>8.250e-01</q_value>\n- <pep>1.000e+00</pep>\n- <exp_mass>741.2000</exp_mass>\n- <calc_mass>741.207</calc_mass>\n- <protein_id>tr|A6ZMU4|A6ZMU4_YEAS7</protein_id>\n- <protein_id>tr|A6ZUB8|A6ZUB8_YEAS7</protein_id>\n- <p_value>1.000e+00</p_value>\n- <psm_ids>\n- <psm_id>trg_2432_1_1</psm_id>\n- </psm_ids>\n- </peptide>\n- <peptide p:peptide_id="DDMDDM" p:decoy="false">\n- <svm_score>-2.473</svm_score>\n- <q_value>8.250e-01</q_value>\n- <pep>1.000e+00</pep>\n- <exp_mass>741.2000</exp_mass>\n- <calc_mass>741.207</calc_mass>\n- <protein_id>tr|A6ZUB8|A6ZUB8_YEAS7</protein_id>\n- <p_value>1.000e+00</p_value>\n- <psm_ids>\n- <psm_id>trg_2376_1_1</psm_id>\n+ <psm_id>dataset_88023_SII_2545_1_2545_6_1</psm_id>\n </psm_ids>\n </peptide>\n </peptides>\n' |
| b |
| diff -r 3a49065a05d6 -r 86770eea5b09 test-data/percolatorTab --- a/test-data/percolatorTab Wed Dec 07 16:43:51 2016 -0500 +++ b/test-data/percolatorTab Sat Mar 04 20:36:03 2017 -0500 |
| [ |
| b'@@ -1,7686 +1,2103 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|
| b |
| diff -r 3a49065a05d6 -r 86770eea5b09 test-data/pool0_metafile --- a/test-data/pool0_metafile Wed Dec 07 16:43:51 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -empty_file_fr1.mzid -empty_file_fr2.mzid |
| b |
| diff -r 3a49065a05d6 -r 86770eea5b09 test-data/pool1_metafile --- a/test-data/pool1_metafile Wed Dec 07 16:43:51 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -empty_file_fr3.mzid -empty_file_fr4.mzid |
| b |
| diff -r 3a49065a05d6 -r 86770eea5b09 test-data/target_ds2_withperco.mzid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/target_ds2_withperco.mzid Sat Mar 04 20:36:03 2017 -0500 |
| b |
| b'@@ -0,0 +1,387 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<MzIdentML id="MS-GF+" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2017-03-01T15:00:34" >\n+<cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">\n+ <cv id="PSI-MS" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.30.0" fullName="PSI-MS"/>\n+ <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/>\n+ <cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" fullName="UNIT-ONTOLOGY"/>\n+</cvList>\n+<AnalysisSoftwareList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">\n+ <AnalysisSoftware version="Beta (v10072)" name="MS-GF+" id="ID_software">\n+ <SoftwareName>\n+ <cvParam 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| b |
| diff -r 3a49065a05d6 -r 86770eea5b09 test-data/target_ds3_withperco.mzid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/target_ds3_withperco.mzid Sat Mar 04 20:36:03 2017 -0500 |
| b |
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