| Previous changeset 7:7414c55d1bff (2018-02-12) Next changeset 9:2e19b070f997 (2019-05-15) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb |
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modified:
readme.md |
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added:
test-data/FileFilter_1_input.mzML test-data/MetaProSIP_1_input.fasta test-data/MetaProSIP_1_input.featureXML test-data/MetaProSIP_1_input.mzML test-data/MetaProSIP_1_output_1.csv test-data/MetaProSIP_1_output_2.csv test-data/MzMLSplitter_output_part1.mzML test-data/MzMLSplitter_output_part2.mzML |
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| diff -r 7414c55d1bff -r 29f7843b3371 readme.md --- a/readme.md Mon Feb 12 13:00:45 2018 -0500 +++ b/readme.md Tue Mar 20 14:51:47 2018 -0400 |
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| @@ -170,16 +170,6 @@ </tests> ``` - - * `This section might not be up to date. It might be worth trying if these tools will run now.` These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in - by the automatic conversion step and are therefore in `tools_blacklist.txt`: - * SeedListGenerator - * SpecLibSearcher - * MapAlignerIdentification - * MapAlignerPoseClustering - * MapAlignerSpectrum - * MapAlignerRTTransformer - * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well: * OMSSAAdapter * MyrimatchAdapter |
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| diff -r 7414c55d1bff -r 29f7843b3371 test-data/FileFilter_1_input.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FileFilter_1_input.mzML Tue Mar 20 14:51:47 2018 -0400 |
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| b'@@ -0,0 +1,336 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1.0">\n+\t<cvList count="2">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+\t\t<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n+\t\t</fileContent>\n+\t\t<contact>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value=", " />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="" />\n+\t\t</contact>\n+\t</fileDescription>\n+\t<sampleList count="1">\n+\t\t<sample id="sa_0" name="">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="12">\n+\t\t<software id="so_in_0" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_default" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_dp_sp_0_pm_0" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_dp_sp_0_pm_1" version="version_string" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000756" name="FileConverter" />\n+\t\t</software>\n+\t</softwareList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="ic_0">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n+\t\t\t<componentList count="3">\n+\t\t\t\t<source order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000008" name="ionization type" />\n+\t\t\t\t</source>\n+\t\t\t\t<analyzer order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000443" name="mass analyzer type" />\n+\t\t\t\t</analyzer>\n+\t\t\t\t<detector order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000026" name="detector type" />\n+\t\t\t\t</detector>\n+\t\t\t</componentList>\n+\t\t\t<softwareRef ref="so_in_0" />\n+\t\t</instrumentConfiguration>\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="10">\n+\t\t<dataProcessing id="dp_sp_0">\n+\t\t\t<processingMethod order="0" softwareRef="so_dp_sp_0_pm_0">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000543" name="data processing action" />\n+\t\t\t</processingMethod>\n+\t\t\t<processingMethod order="0" softwareRef="so_dp_sp_0_pm_1">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:10'..b'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</binary>\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n' |
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| diff -r 7414c55d1bff -r 29f7843b3371 test-data/MetaProSIP_1_input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MetaProSIP_1_input.fasta Tue Mar 20 14:51:47 2018 -0400 |
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| @@ -0,0 +1,6 @@ +>contig23640_802236 length=2326 numreads=28 strand:-1 frame:0 orf_location:136:990 +GGIPNEENWNFGSSDGSGLPVRGSGQRRDVLGRLCRRNFTSSIGQSVNVRDVEASGFAGG +MSRYHFKYGGAVDPTVLGGVKLGTWFVKEGFAGWSGYPDWCKYFGFYTDFSYHRFYTRDN +RISGTDFFAAYGGGSAALGDVGFMKTEGMVATWAFMLAARYGFFQDSEVPFGRLQPYVAV +GPAIMFSSMKPKIWTQFNEPNVGFPNPDLVYSPGNQSSTDLGLAVDTGIRYMCLKNVSLD +ISFKYRYAQPHYNFSGQDGSVMVPAHMSLSPALNLYSFQAGVAYHF |
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| diff -r 7414c55d1bff -r 29f7843b3371 test-data/MetaProSIP_1_input.featureXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MetaProSIP_1_input.featureXML Tue Mar 20 14:51:47 2018 -0400 |
| [ |
| b'@@ -0,0 +1,129 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<featureMap version="1.9" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/FeatureXML_1_9.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">\n+\t<dataProcessing completion_time="2017-12-08T12:44:40">\n+\t\t<software name="FileFilter" version="2.3.0" />\n+\t\t<processingAction name="Data filtering" />\n+\t\t<UserParam type="string" name="parameter: in" value="MetaProSIP_1_input.featureXML"/>\n+\t\t<UserParam type="string" name="parameter: in_type" value=""/>\n+\t\t<UserParam type="string" name="parameter: out" value="MetaProSIP_1_input.featureXML"/>\n+\t\t<UserParam type="string" name="parameter: out_type" value=""/>\n+\t\t<UserParam type="string" name="parameter: rt" value=":"/>\n+\t\t<UserParam type="string" name="parameter: mz" value=":"/>\n+\t\t<UserParam type="string" name="parameter: int" value=":"/>\n+\t\t<UserParam type="string" name="parameter: sort" value="false"/>\n+\t\t<UserParam type="string" name="parameter: log" value=""/>\n+\t\t<UserParam type="int" name="parameter: debug" value="0"/>\n+\t\t<UserParam type="int" name="parameter: threads" value="1"/>\n+\t\t<UserParam type="string" name="parameter: no_progress" value="false"/>\n+\t\t<UserParam type="string" name="parameter: force" value="false"/>\n+\t\t<UserParam type="string" name="parameter: test" value="false"/>\n+\t\t<UserParam type="float" name="parameter: peak_options:sn" value="0"/>\n+\t\t<UserParam type="intList" name="parameter: peak_options:rm_pc_charge" value="[]"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:pc_mz_range" value=":"/>\n+\t\t<UserParam type="floatList" name="parameter: peak_options:pc_mz_list" value="[]"/>\n+\t\t<UserParam type="intList" name="parameter: peak_options:level" value="[1, 2, 3]"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:sort_peaks" value="false"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:no_chromatograms" value="false"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:remove_chromatograms" value="false"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:mz_precision" value="64"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:int_precision" value="32"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:indexed_file" value="false"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:zlib_compression" value="false"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:numpress:masstime" value="none"/>\n+\t\t<UserParam type="float" name="parameter: peak_options:numpress:masstime_error" value="0.0001"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:numpress:intensity" value="none"/>\n+\t\t<UserParam type="float" name="parameter: peak_options:numpress:intensity_error" value="0.0001"/>\n+\t\t<UserParam type="string" name="parameter: spectra:remove_zoom" value="false"/>\n+\t\t<UserParam type="string" name="parameter: spectra:remove_mode" value=""/>\n+\t\t<UserParam type="string" name="parameter: spectra:remove_activation" value=""/>\n+\t\t<UserParam type="string" name="parameter: spectra:remove_collision_energy" value=":"/>\n+\t\t<UserParam type="string" name="parameter: spectra:remove_isolation_window_width" value=":"/>\n+\t\t<UserParam type="string" name="parameter: spectra:select_zoom" value="false"/>\n+\t\t<UserParam type="string" name="parameter: spectra:select_mode" value=""/>\n+\t\t<UserParam type="string" name="parameter: spectra:select_activation" value=""/>\n+\t\t<UserParam type="string" name="parameter: spectra:select_collision_energy" value=":"/>\n+\t\t<UserParam type="string" name="parameter: spectra:select_isolation_window_width" value=":"/>\n+\t\t<UserParam type="string" name="parameter: spectra:select_polarity" value=""/>\n+\t\t<UserParam type="string" name="parameter: feature:q" value=":"/>\n+\t\t<UserParam type="intList" name="parameter: consensus:map" value="[]"/>\n+\t\t<UserParam type="string" name="parameter: consensus:map_and" value="false"/>\n+\t\t<UserParam type="string" name="parameter: consensus:blackorwhitelist:bl'..b'id:remove_unannotated_features" value="true"/>\n+\t\t<UserParam type="string" name="parameter: id:remove_unassigned_ids" value="false"/>\n+\t\t<UserParam type="string" name="parameter: id:blacklist" value=""/>\n+\t\t<UserParam type="float" name="parameter: id:rt" value="0.1"/>\n+\t\t<UserParam type="float" name="parameter: id:mz" value="0.001"/>\n+\t\t<UserParam type="string" name="parameter: id:blacklist_imperfect" value="false"/>\n+\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:max_intensity" value="-1"/>\n+\t\t<UserParam type="float" name="parameter: algorithm:SignalToNoise:auto_max_stdev_factor" value="3"/>\n+\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_max_percentile" value="95"/>\n+\t\t<UserParam type="int" 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