Mercurial > repos > galaxyp > openms_peptideindexer
annotate prepare_test_data_manual.sh @ 13:69332aa5fa11 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
| author | galaxyp |
|---|---|
| date | Thu, 27 Aug 2020 22:45:34 +0000 |
| parents | |
| children | c98b4e5b2e83 |
| rev | line source |
|---|---|
|
13
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
1 MSSimulator -test -in DecoyDatabase_1.fasta -out MSsimulator.mzml -algorithm:RandomNumberGenerators:biological reproducible -algorithm:RandomNumberGenerators:technical reproducible > MSSimulator_1.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
2 if [[ "$?" -ne "0" ]]; then >&2 echo 'MSSimulator_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
3 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
4 MSSimulator -test -in DecoyDatabase_1.fasta -out MSsimulator_MALDI.mzml -algorithm:RandomNumberGenerators:biological reproducible -algorithm:RandomNumberGenerators:technical reproducible -algorithm:MSSim:Global:ionization_type MALDI > MSSimulator_2.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
5 if [[ "$?" -ne "0" ]]; then >&2 echo 'MSSimulator_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
6 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
7 ClusterMassTracesByPrecursor -test -in_ms1 ConsensusMapNormalizer_input.consensusXML -in_swath ConsensusMapNormalizer_input.consensusXML -out ClusterMassTracesByPrecursor.mzml > ClusterMassTracesByPrecursor.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
8 if [[ "$?" -ne "0" ]]; then >&2 echo 'ClusterMassTracesByPrecursor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
9 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
10 ClusterMassTraces -test -in ConsensusMapNormalizer_input.consensusXML -out ClusterMassTraces.mzml > ClusterMassTraces.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
11 if [[ "$?" -ne "0" ]]; then >&2 echo 'ClusterMassTraces failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
12 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
13 CVInspector -test -cv_files CHEMISTRY/XLMOD.obo -cv_names XLMOD -mapping_file MAPPING/ms-mapping.xml -html CVInspector.html > CVInspector.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
14 if [[ "$?" -ne "0" ]]; then >&2 echo 'CVInspector failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
15 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
16 DeMeanderize -test -in MSsimulator_MALDI.mzml -out DeMeanderize.mzml > DeMeanderize.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
17 if [[ "$?" -ne "0" ]]; then >&2 echo 'DeMeanderize failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
18 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
19 # TODO DigestorMotif |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
20 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
21 Digestor -test -in random.fa -out Digestor.fasta -out_type fasta > Digestor.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
22 if [[ "$?" -ne "0" ]]; then >&2 echo 'Digestor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
23 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
24 EICExtractor -test -in spectra.mzML -pos FileConverter_10_input.edta -out EICExtractor.csv > EICExtractor.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
25 if [[ "$?" -ne "0" ]]; then >&2 echo 'EICExtractor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
26 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
27 #TODO ERPairFinder |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
28 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
29 FeatureFinderIsotopeWavelet -test -in FeatureFinderCentroided_1_input.mzML -out FeatureFinderIsotopeWavelet.featureXML > FeatureFinderIsotopeWavelet.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
30 if [[ "$?" -ne "0" ]]; then >&2 echo 'FeatureFinderIsotopeWavelet failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
31 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
32 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
33 FFEval -test -in FeatureFinderCentroided_1_output.featureXML -truth FeatureFinderCentroided_1_output.featureXML -out FFEval.featureXML -out_roc FFEval_roc.csv > FFEval.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
34 if [[ "$?" -ne "0" ]]; then >&2 echo 'FFEval failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
35 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
36 # TODO? deprecated IDDecoyProbability |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
37 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
38 IDExtractor -test -in MSGFPlusAdapter_1_out.idXML -best_hits -number_of_peptides 1 -out IDExtractor.idXML > IDExtractor.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
39 if [[ "$?" -ne "0" ]]; then >&2 echo 'IDExtractor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
40 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
41 LabeledEval -test -in FeatureLinkerLabeled_1_input.featureXML -truth FeatureLinkerLabeled_1_output.consensusXML> LabeledEval.txt > LabeledEval.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
42 if [[ "$?" -ne "0" ]]; then >&2 echo 'LabeledEval failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
43 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
44 MapStatistics -test -in SiriusAdapter_3_input.featureXML -out MapStatistics.txt > MapStatistics_1.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
45 if [[ "$?" -ne "0" ]]; then >&2 echo 'MapStatistics_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
46 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
47 MapStatistics -test -in ConsensusXMLFile_1.consensusXML -out MapStatistics2.txt > MapStatistics_2.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
48 if [[ "$?" -ne "0" ]]; then >&2 echo 'MapStatistics_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
49 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
50 MetaboliteAdductDecharger -test -in Decharger_input.featureXML -out_cm MetaboliteAdductDecharger_cm.consensusXML -out_fm MetaboliteAdductDecharger_fm.featureXML -outpairs MetaboliteAdductDecharger_pairs.consensusXML > MetaboliteAdductDecharger.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
51 if [[ "$?" -ne "0" ]]; then >&2 echo 'MetaboliteAdductDecharger failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
52 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
53 MetaboliteSpectralMatcher -test -in spectra.mzML -database MetaboliteSpectralDB.mzML -out MetaboliteSpectralMatcher.mzTab > MetaboliteSpectralMatcher.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
54 if [[ "$?" -ne "0" ]]; then >&2 echo 'MetaboliteSpectralMatcher failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
55 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
56 # TODO MRMPairFinder |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
57 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
58 # TODO OpenSwathDIAPreScoring |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
59 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
60 OpenSwathRewriteToFeatureXML -featureXML OpenSwathFeatureXMLToTSV_input.featureXML -out OpenSwathRewriteToFeatureXML.featureXML > OpenSwathRewriteToFeatureXML.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
61 # if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathRewriteToFeatureXML failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
62 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
63 # adapted from the commented tests in OpenMS TODO may be removed later https://github.com/OpenMS/OpenMS/issues/4719 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
64 FileConverter -in PepNovo.mzXML -out PepNovo_1.mzML > /dev/null 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
65 if [[ "$?" -ne "0" ]]; then >&2 echo 'FileConverter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
66 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
67 PepNovoAdapter -ini PepNovoAdapter_1_parameters.ini -in PepNovo_1.mzML -out PepNovoAdapter_3_output.idXML -model_directory pepnovo_models/ -pepnovo_executable pepnovo > PepNovo_1.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
68 if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
69 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
70 FileConverter -in PepNovo.mzData -out PepNovo_4.mzML > /dev/null 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
71 if [[ "$?" -ne "0" ]]; then >&2 echo 'FileConverter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
72 PepNovoAdapter -ini PepNovoAdapter_1_parameters.ini -in PepNovo_4.mzML -out PepNovoAdapter_4_output.idXML -model_directory pepnovo_models/ -pepnovo_executable pepnovo > PepNovo_1.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
73 if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
74 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
75 #PepNovoAdapter -ini PepNovoAdapter_5_parameters.ini -in PepNovoAdapter_5_output.pepnovo_out -out PepNovoAdapter_5_output.idXML -model_directory pepnovo_models/ |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
76 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
77 # TODO PhosphoScoring |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
78 PhosphoScoring -in spectra.mzML -id MSGFPlusAdapter_1_out1.tmp -out PhosphoScoring.idxml > PhosphoScoring.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
79 if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
80 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
81 PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.idxml > PSMFeatureExtractor_1.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
82 if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
83 PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.mzid > PSMFeatureExtractor_2.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
84 if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
85 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
86 QCCalculator -test -in OpenPepXL_input.mzML -out QCCalculator1.qcML > QCCalculator_1.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
87 if [[ "$?" -ne "0" ]]; then >&2 echo 'QCCalculator_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
88 QCCalculator -test -in OpenPepXL_input.mzML -id OpenPepXL_output.idXML -consensus OpenPepXL_input.consensusXML -out QCCalculator2.qcML > QCCalculator_2.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
89 if [[ "$?" -ne "0" ]]; then >&2 echo 'QCCalculator_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
90 QCCalculator -test -in IDMapper_4_input.mzML -id IDMapper_4_input.idXML -feature IDMapper_4_input.featureXML -out QCCalculator3.qcML > QCCalculator_3.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
91 if [[ "$?" -ne "0" ]]; then >&2 echo 'QCCalculator_3 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
92 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
93 # TODO QCEmbedder |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
94 # TODO QCExporter |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
95 # TODO QCExtractor |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
96 # TODO QCImporter |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
97 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
98 QCMerger -test -in QCCalculator1.qcML QCCalculator3.qcML -out QCMerger.qcML > QCMerger.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
99 if [[ "$?" -ne "0" ]]; then >&2 echo 'QCMerger failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
100 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
101 QCShrinker -test -in QCCalculator1.qcML -out QCShrinker.qcML > QCShrinker.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
102 if [[ "$?" -ne "0" ]]; then >&2 echo 'QCShrinker failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
103 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
104 RNADigestor -test -in random_RNA.fa -out RNADigestor.fasta > RNADigestor.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
105 if [[ "$?" -ne "0" ]]; then >&2 echo 'RNADigestor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
106 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
107 RNPxlXICFilter -test -control FileFilter_1_input.mzML -treatment FileFilter_1_input.mzML -out RNPxlXICFilter.mzML > RNPxlXICFilter.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
108 if [[ "$?" -ne "0" ]]; then >&2 echo 'RNPxlXICFilter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
109 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
110 # TODO out should be tsv, but needs https://github.com/OpenMS/OpenMS/pull/4533 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
111 RTEvaluation -in PeptideIndexer_1.idXML -out RTEvaluation.csv > RTEvaluation.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
112 if [[ "$?" -ne "0" ]]; then >&2 echo 'RTEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
113 ln -fs RTEvaluation.csv RTEvaluation.tsv > .stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
114 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
115 SemanticValidator -test -in FileFilter_1_input.mzML -mapping_file MAPPING/ms-mapping.xml > SemanticValidator.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
116 if [[ "$?" -ne "0" ]]; then >&2 echo 'SemanticValidator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
117 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
118 IDFilter -in PeptideIndexer_1.idXML -best:strict -out SequenceCoverageCalculator_1.idXML > IDFilter.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
119 if [[ "$?" -ne "0" ]]; then >&2 echo 'IDFilter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
120 SequenceCoverageCalculator -test -in_database PeptideIndexer_1.fasta -in_peptides SequenceCoverageCalculator_1.idXML -out SequenceCoverageCalculator.txt > SequenceCoverageCalculator.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
121 if [[ "$?" -ne "0" ]]; then >&2 echo 'SequenceCoverageCalculator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
122 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
123 # TODO SpecLibCreator |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
124 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
125 SpectraFilterBernNorm -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterBernNorm.mzML > SpectraFilterBernNorm.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
126 if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterBernNorm failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
127 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
128 SpectraFilterMarkerMower -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterMarkerMower.mzML > SpectraFilterMarkerMower.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
129 if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterMarkerMower failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
130 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
131 SpectraFilterNLargest -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterNLargest.mzML > SpectraFilterNLargest.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
132 if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterNLargest failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
133 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
134 SpectraFilterNormalizer -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterNormalizer.mzML > SpectraFilterNormalizer.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
135 if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterNormalizer failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
136 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
137 SpectraFilterParentPeakMower -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterParentPeakMower.mzML > SpectraFilterParentPeakMower.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
138 if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterParentPeakMower failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
139 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
140 SpectraFilterScaler -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterScaler.mzML > SpectraFilterScaler.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
141 if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterScaler failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
142 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
143 SpectraFilterThresholdMower -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterThresholdMower.mzML > SpectraFilterThresholdMower.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
144 if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterThresholdMower failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
145 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
146 SpectraMerger -test -in NovorAdapter_in.mzML -out SpectraMerger_1.mzML > SpectraMerger.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
147 if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraMerger failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
148 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
149 # TODO SvmTheoreticalSpectrumGeneratorTrainer |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
150 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
151 TransformationEvaluation -test -in FileInfo_16_input.trafoXML -out TransformationEvaluation.trafoXML > TransformationEvaluation.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
152 if [[ "$?" -ne "0" ]]; then >&2 echo 'TransformationEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
153 |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
154 XMLValidator -test -in FileFilter_1_input.mzML > XMLValidator.stdout 2> stderr |
|
69332aa5fa11
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff
changeset
|
155 if [[ "$?" -ne "0" ]]; then >&2 echo 'XMLValidator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi |