Mercurial > repos > galaxyp > openms_cruxadapter

comparison prepare_test_data_manual.sh @ 2:aed7aeb6feec draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:05:24 +0000
parents a8dd6f1257ab
children a915cadc2f07
comparison
equal deleted inserted replaced
1:60b24c30af7d 2:aed7aeb6feec
53 MetaboliteSpectralMatcher -test -in spectra.mzML -database MetaboliteSpectralDB.mzML -out MetaboliteSpectralMatcher.mzTab > MetaboliteSpectralMatcher.stdout 2> stderr 53 MetaboliteSpectralMatcher -test -in spectra.mzML -database MetaboliteSpectralDB.mzML -out MetaboliteSpectralMatcher.mzTab > MetaboliteSpectralMatcher.stdout 2> stderr
54 if [[ "$?" -ne "0" ]]; then >&2 echo 'MetaboliteSpectralMatcher failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi 54 if [[ "$?" -ne "0" ]]; then >&2 echo 'MetaboliteSpectralMatcher failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
55 55
56 # TODO MRMPairFinder 56 # TODO MRMPairFinder
57 57
58 # TODO OpenSwathDIAPreScoring 58 # generate two inputs for OpenSwathDIAPreScoring
59 OpenSwathDIAPreScoring -tr OpenSwathWorkflow_1_input.TraML -swath_files OpenSwathAnalyzer_2_swathfile.mzML -output_files OpenSwathDIAPreScoring.tsv > OpenSwathDIAPreScoring.stdout 2> stderr
60 if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathDIAPreScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
61
62 # generate two inputs for OpenSwathDIAPreScoring by linking
63 ln -s OpenSwathAnalyzer_2_swathfile.mzML OpenSwathDIAPreScoring_in1.mzML
64 ln -s OpenSwathAnalyzer_2_swathfile.mzML OpenSwathDIAPreScoring_in2.mzML
65 OpenSwathDIAPreScoring -tr OpenSwathWorkflow_1_input.TraML -swath_files OpenSwathDIAPreScoring_in1.mzML OpenSwathDIAPreScoring_in2.mzML -output_files OpenSwathDIAPreScoring_2_1.tsv OpenSwathDIAPreScoring_2_2.tsv > OpenSwathDIAPreScoring.stdout 2> stderr
66 if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathDIAPreScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
59 67
60 OpenSwathRewriteToFeatureXML -featureXML OpenSwathFeatureXMLToTSV_input.featureXML -out OpenSwathRewriteToFeatureXML.featureXML > OpenSwathRewriteToFeatureXML.stdout 2> stderr 68 OpenSwathRewriteToFeatureXML -featureXML OpenSwathFeatureXMLToTSV_input.featureXML -out OpenSwathRewriteToFeatureXML.featureXML > OpenSwathRewriteToFeatureXML.stdout 2> stderr
61 # if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathRewriteToFeatureXML failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi 69 # if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathRewriteToFeatureXML failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
62 70
63 # adapted from the commented tests in OpenMS TODO may be removed later https://github.com/OpenMS/OpenMS/issues/4719 71 # adapted from the commented tests in OpenMS TODO may be removed later https://github.com/OpenMS/OpenMS/issues/4719
105 if [[ "$?" -ne "0" ]]; then >&2 echo 'RNADigestor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi 113 if [[ "$?" -ne "0" ]]; then >&2 echo 'RNADigestor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
106 114
107 RNPxlXICFilter -test -control FileFilter_1_input.mzML -treatment FileFilter_1_input.mzML -out RNPxlXICFilter.mzML > RNPxlXICFilter.stdout 2> stderr 115 RNPxlXICFilter -test -control FileFilter_1_input.mzML -treatment FileFilter_1_input.mzML -out RNPxlXICFilter.mzML > RNPxlXICFilter.stdout 2> stderr
108 if [[ "$?" -ne "0" ]]; then >&2 echo 'RNPxlXICFilter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi 116 if [[ "$?" -ne "0" ]]; then >&2 echo 'RNPxlXICFilter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
109 117
110 # TODO out should be tsv, but needs https://github.com/OpenMS/OpenMS/pull/4533 118 RTEvaluation -in PeptideIndexer_1.idXML -out RTEvaluation.tsv > RTEvaluation.stdout 2> stderr
111 RTEvaluation -in PeptideIndexer_1.idXML -out RTEvaluation.csv > RTEvaluation.stdout 2> stderr
112 if [[ "$?" -ne "0" ]]; then >&2 echo 'RTEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi 119 if [[ "$?" -ne "0" ]]; then >&2 echo 'RTEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
113 ln -fs RTEvaluation.csv RTEvaluation.tsv > .stdout 2> stderr
114 120
115 SemanticValidator -test -in FileFilter_1_input.mzML -mapping_file MAPPING/ms-mapping.xml > SemanticValidator.stdout 2> stderr 121 SemanticValidator -test -in FileFilter_1_input.mzML -mapping_file MAPPING/ms-mapping.xml > SemanticValidator.stdout 2> stderr
116 if [[ "$?" -ne "0" ]]; then >&2 echo 'SemanticValidator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi 122 if [[ "$?" -ne "0" ]]; then >&2 echo 'SemanticValidator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
117 123
118 IDFilter -in PeptideIndexer_1.idXML -best:strict -out SequenceCoverageCalculator_1.idXML > IDFilter.stdout 2> stderr 124 IDFilter -in PeptideIndexer_1.idXML -best:strict -out SequenceCoverageCalculator_1.idXML > IDFilter.stdout 2> stderr