annotate prepare_test_data.sh @ 12:f918cb7aefd5 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author galaxyp
date Thu, 24 Sep 2020 12:27:04 +0000
parents 65be0674bb70
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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11
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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1 export COMET_BINARY="comet"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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2 export CRUX_BINARY="crux"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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3 export FIDOCHOOSEPARAMS_BINARY="FidoChooseParameters"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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4 export FIDO_BINARY="Fido"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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5 export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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6 export MARACLUSTER_BINARY="/tmp/openms-stuff//OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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7 export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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8 export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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9 export MYRIMATCH_BINARY="myrimatch"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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10 export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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11 export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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12 export PERCOLATOR_BINARY="percolator"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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13 export SIRIUS_BINARY="$(which sirius)"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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14 export SPECTRAST_BINARY="spectrast"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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15 export XTANDEM_BINARY="xtandem"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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16 export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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17 FuzzyDiff -test -ini FuzzyDiff.ini -in1 FuzzyDiff_3_in1.featureXML -in2 FuzzyDiff_3_in2.featureXML > UTILS_FuzzyDiff_3.stdout 2> UTILS_FuzzyDiff_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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18 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_FuzzyDiff_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_FuzzyDiff_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_FuzzyDiff_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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19 IDMerger -test -in IDMerger_1_input1.idXML IDMerger_1_input2.idXML -out IDMerger_1_output.tmp -annotate_file_origin > TOPP_IDMerger_1.stdout 2> TOPP_IDMerger_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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20 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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21 IDMerger -test -pepxml_protxml -in IDMerger_2_input1.idXML IDMerger_2_input2.idXML -out IDMerger_2_output.tmp > TOPP_IDMerger_2.stdout 2> TOPP_IDMerger_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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22 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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23 IDMerger -test -in IDMerger_1_input1.idXML IDMerger_1_input1.idXML -out IDMerger_3_output.tmp > TOPP_IDMerger_3.stdout 2> TOPP_IDMerger_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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24 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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25 IDMerger -test -in degenerated_empty.idXML degenerated_empty.idXML -out IDMerger_4_output.tmp > TOPP_IDMerger_4.stdout 2> TOPP_IDMerger_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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26 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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27 IDMerger -test -in IDMerger_2_input1.idXML -add_to IDMerger_5_input1.idXML -out IDMerger_5_output.tmp > TOPP_IDMerger_5.stdout 2> TOPP_IDMerger_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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28 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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29 BaselineFilter -test -in BaselineFilter_input.mzML -out BaselineFilter.tmp -struc_elem_length 1.5 > TOPP_BaselineFilter_1.stdout 2> TOPP_BaselineFilter_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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30 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_BaselineFilter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_BaselineFilter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_BaselineFilter_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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31 ConsensusMapNormalizer -test -in ConsensusMapNormalizer_input.consensusXML -out ConsensusMapNormalizer.tmp > TOPP_ConsensusMapNormalizer_1.stdout 2> TOPP_ConsensusMapNormalizer_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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32 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusMapNormalizer_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusMapNormalizer_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConsensusMapNormalizer_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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33 MapNormalizer -test -in MapNormalizer_input.mzML -out MapNormalizer.tmp > TOPP_MapNormalizer_1.stdout 2> TOPP_MapNormalizer_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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34 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapNormalizer_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapNormalizer_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapNormalizer_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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35 Decharger -test -in Decharger_input.featureXML -ini Decharger_input.ini -out_fm Decharger_output_fm.tmp -out_cm Decharger_output.tmp -outpairs Decharger_p_output.tmp > TOPP_Decharger_1.stdout 2> TOPP_Decharger_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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36 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_Decharger_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_Decharger_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_Decharger_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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37 DTAExtractor -test -in DTAExtractor_1_input.mzML -out DTAExtractor -rt :61 > TOPP_DTAExtractor_1.stdout 2> TOPP_DTAExtractor_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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38 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_DTAExtractor_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_DTAExtractor_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_DTAExtractor_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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39 DTAExtractor -test -in DTAExtractor_1_input.mzML -out DTAExtractor -level 1 > TOPP_DTAExtractor_2.stdout 2> TOPP_DTAExtractor_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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40 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_DTAExtractor_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_DTAExtractor_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_DTAExtractor_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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41 DTAExtractor -test -in DTAExtractor_1_input.mzML -out DTAExtractor -level 2 -mz :1000 > TOPP_DTAExtractor_3.stdout 2> TOPP_DTAExtractor_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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42 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_DTAExtractor_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_DTAExtractor_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_DTAExtractor_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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43 MassTraceExtractor -test -ini MassTraceExtractor.ini -in MassTraceExtractor_1_input.mzML -out MassTraceExtractor_1.tmp > TOPP_MassTraceExtractor_1.stdout 2> TOPP_MassTraceExtractor_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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44 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MassTraceExtractor_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MassTraceExtractor_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MassTraceExtractor_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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45 MassTraceExtractor -test -ini MassTraceExtractor_2.ini -in MassTraceExtractor_1_input.mzML -out MassTraceExtractor_2.tmp > TOPP_MassTraceExtractor_2.stdout 2> TOPP_MassTraceExtractor_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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46 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MassTraceExtractor_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MassTraceExtractor_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MassTraceExtractor_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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47 FeatureFinderMetabo -test -ini FeatureFinderMetabo.ini -in FeatureFinderMetabo_1_input.mzML -out FeatureFinderMetabo_1.tmp > TOPP_FeatureFinderMetabo_1.stdout 2> TOPP_FeatureFinderMetabo_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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48 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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49 FeatureFinderMetabo -test -ini FeatureFinderMetabo_2_noEPD.ini -in FeatureFinderMetabo_2_input.mzML -out FeatureFinderMetabo_2.tmp > TOPP_FeatureFinderMetabo_2.stdout 2> TOPP_FeatureFinderMetabo_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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50 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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51 FeatureFinderMetabo -test -ini FeatureFinderMetabo_3.ini -in FeatureFinderMetabo_3_input.mzML -out FeatureFinderMetabo_3.tmp -out_chrom FeatureFinderMetabo_3_chrom.tmp > TOPP_FeatureFinderMetabo_3.stdout 2> TOPP_FeatureFinderMetabo_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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52 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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53 FeatureFinderMetabo -test -ini FeatureFinderMetabo_4.ini -in FeatureFinderMetabo_3_input.mzML -out FeatureFinderMetabo_4.tmp -out_chrom FeatureFinderMetabo_4_chrom.tmp > TOPP_FeatureFinderMetabo_4.stdout 2> TOPP_FeatureFinderMetabo_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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54 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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55 FeatureFinderMetabo -test -ini FeatureFinderMetabo.ini -in FeatureFinderMetabo_1_input.mzML -out FeatureFinderMetabo_5.tmp -algorithm:mtd:quant_method max_height > TOPP_FeatureFinderMetabo_5.stdout 2> TOPP_FeatureFinderMetabo_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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56 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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57 FeatureFinderCentroided -test -ini FeatureFinderCentroided_1_parameters.ini -in FeatureFinderCentroided_1_input.mzML -out FeatureFinderCentroided_1.tmp > TOPP_FeatureFinderCentroided_1.stdout 2> TOPP_FeatureFinderCentroided_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
58 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderCentroided_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderCentroided_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderCentroided_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
59 FeatureFinderIdentification -test -in FeatureFinderIdentification_1_input.mzML -id FeatureFinderIdentification_1_input.idXML -out FeatureFinderIdentification_1.tmp -extract:mz_window 0.1 -detect:peak_width 60 -model:type none > TOPP_FeatureFinderIdentification_1.stdout 2> TOPP_FeatureFinderIdentification_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
60 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderIdentification_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderIdentification_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderIdentification_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
61 FeatureFinderIdentification -test -in FeatureFinderIdentification_1_input.mzML -id FeatureFinderIdentification_1_input.idXML -out FeatureFinderIdentification_3.tmp -extract:mz_window 0.1 -detect:peak_width 60 -model:type symmetric > TOPP_FeatureFinderIdentification_3.stdout 2> TOPP_FeatureFinderIdentification_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
62 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderIdentification_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderIdentification_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderIdentification_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
63 FeatureFinderIdentification -test -in FeatureFinderIdentification_1_input.mzML -id FeatureFinderIdentification_1_input.idXML -out FeatureFinderIdentification_4.tmp -extract:mz_window 0.1 -extract:batch_size 10 -detect:peak_width 60 -model:type none > TOPP_FeatureFinderIdentification_4.stdout 2> TOPP_FeatureFinderIdentification_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
64 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderIdentification_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderIdentification_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderIdentification_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
65 FeatureFinderMRM -test -in FeatureFinderMRM_1_input.mzML -ini FeatureFinderMRM_1_parameters.ini -out FeatureFinderMRM_1.tmp > TOPP_FeatureFinderMRM_1.stdout 2> TOPP_FeatureFinderMRM_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
66 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMRM_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMRM_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMRM_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
67 FeatureFinderMultiplex -test -in FeatureFinderMultiplex_1_input.mzML -ini FeatureFinderMultiplex_1_parameters.ini -out FeatureFinderMultiplex_1.tmp -out_multiplets FeatureFinderMultiplex_2.tmp > TOPP_FeatureFinderMultiplex_1.stdout 2> TOPP_FeatureFinderMultiplex_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
68 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
69 FeatureFinderMultiplex -test -in FeatureFinderMultiplex_2_input.mzML -ini FeatureFinderMultiplex_2_parameters.ini -out FeatureFinderMultiplex_3.tmp -out_multiplets FeatureFinderMultiplex_4.tmp > TOPP_FeatureFinderMultiplex_2.stdout 2> TOPP_FeatureFinderMultiplex_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
70 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
71 FeatureFinderMultiplex -test -in FeatureFinderMultiplex_3_input.mzML -ini FeatureFinderMultiplex_3_parameters.ini -out FeatureFinderMultiplex_5.tmp -out_multiplets FeatureFinderMultiplex_6.tmp > TOPP_FeatureFinderMultiplex_3.stdout 2> TOPP_FeatureFinderMultiplex_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
72 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
73 FeatureFinderMultiplex -test -in FeatureFinderMultiplex_4_input.mzML -ini FeatureFinderMultiplex_4_parameters.ini -out FeatureFinderMultiplex_7.tmp -out_multiplets FeatureFinderMultiplex_8.tmp > TOPP_FeatureFinderMultiplex_4.stdout 2> TOPP_FeatureFinderMultiplex_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
74 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
75 FeatureFinderMultiplex -test -in FeatureFinderMultiplex_5_input.mzML -ini FeatureFinderMultiplex_5_parameters.ini -out FeatureFinderMultiplex_9.tmp -out_multiplets FeatureFinderMultiplex_10.tmp > TOPP_FeatureFinderMultiplex_5.stdout 2> TOPP_FeatureFinderMultiplex_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
76 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
77 FeatureFinderMultiplex -test -in FeatureFinderMultiplex_6_input.mzML -ini FeatureFinderMultiplex_6_parameters.ini -out FeatureFinderMultiplex_11.tmp -out_multiplets FeatureFinderMultiplex_12.tmp > TOPP_FeatureFinderMultiplex_6.stdout 2> TOPP_FeatureFinderMultiplex_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
78 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
79 FeatureFinderMultiplex -test -in FeatureFinderMultiplex_7_input.mzML -ini FeatureFinderMultiplex_7_parameters.ini -out FeatureFinderMultiplex_13.tmp -out_multiplets FeatureFinderMultiplex_14.tmp > TOPP_FeatureFinderMultiplex_7.stdout 2> TOPP_FeatureFinderMultiplex_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
80 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
81 FeatureFinderMultiplex -test -in FeatureFinderMultiplex_8_input.mzML -ini FeatureFinderMultiplex_8_parameters.ini -out FeatureFinderMultiplex_15.tmp -out_multiplets FeatureFinderMultiplex_16.tmp > TOPP_FeatureFinderMultiplex_8.stdout 2> TOPP_FeatureFinderMultiplex_8.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
82 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_8.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
83 FeatureFinderMultiplex -test -in FeatureFinderMultiplex_9_input.mzML -ini FeatureFinderMultiplex_9_parameters.ini -out FeatureFinderMultiplex_17.tmp -out_multiplets FeatureFinderMultiplex_18.tmp > TOPP_FeatureFinderMultiplex_9.stdout 2> TOPP_FeatureFinderMultiplex_9.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
84 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_9.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
85 FeatureFinderMultiplex -test -in FeatureFinderMultiplex_10_input.mzML -ini FeatureFinderMultiplex_10_parameters.ini -out FeatureFinderMultiplex_19.tmp -out_multiplets FeatureFinderMultiplex_20.tmp > TOPP_FeatureFinderMultiplex_10.stdout 2> TOPP_FeatureFinderMultiplex_10.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
86 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_10.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
87 FeatureFinderMultiplex -test -in FeatureFinderMultiplex_11_input.mzML -ini FeatureFinderMultiplex_11_parameters.ini -out FeatureFinderMultiplex_21.tmp > TOPP_FeatureFinderMultiplex_11.stdout 2> TOPP_FeatureFinderMultiplex_11.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
88 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_11.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
89 FileConverter -test -in FileConverter_1_input.mzData -out FileConverter_1.tmp -out_type mzML > TOPP_FileConverter_1.stdout 2> TOPP_FileConverter_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
90 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
91 FileConverter -test -in FileConverter_2_input.someInputDTA2D -in_type dta2d -out FileConverter_2.tmp -out_type mzML > TOPP_FileConverter_2.stdout 2> TOPP_FileConverter_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
92 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
93 FileConverter -test -in FileConverter_3_input.featureXML -out FileConverter_3.tmp -out_type mzML > TOPP_FileConverter_3.stdout 2> TOPP_FileConverter_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
94 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
95 FileConverter -test -in FileConverter_4_input.mzXML -out FileConverter_4.tmp -out_type mzML > TOPP_FileConverter_4.stdout 2> TOPP_FileConverter_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
96 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
97 FileConverter -test -in FileConverter_5_input.mzML -out FileConverter_5.tmp -out_type mzXML > TOPP_FileConverter_5.stdout 2> TOPP_FileConverter_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
98 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
99 FileConverter -test -in FileConverter_6_input.mzML -out FileConverter_6.tmp -out_type mzXML > TOPP_FileConverter_6.stdout 2> TOPP_FileConverter_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
100 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
101 FileConverter -test -in FileConverter_7_input.consensusXML -out FileConverter_7.tmp -out_type featureXML > TOPP_FileConverter_7.stdout 2> TOPP_FileConverter_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
102 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
103 FileConverter -test -in FileConverter_8_input.mzML -out FileConverter_8.tmp -out_type mzData > TOPP_FileConverter_8.stdout 2> TOPP_FileConverter_8.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
104 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_8.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
105 FileConverter -test -in FileConverter_9_input.consensusXML -out FileConverter_9.tmp -out_type featureXML > TOPP_FileConverter_9.stdout 2> TOPP_FileConverter_9.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
106 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_9.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
107 FileConverter -test -in FileConverter_10_input.edta -no_progress -out FileConverter_10.tmp -out_type featureXML > TOPP_FileConverter_10.stdout 2> TOPP_FileConverter_10.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
108 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_10.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
109 FileConverter -test -in FileConverter_11_input.peplist -no_progress -out FileConverter_11.tmp -out_type featureXML > TOPP_FileConverter_11.stdout 2> TOPP_FileConverter_11.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
110 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_11.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
111 FileConverter -test -in FileConverter_12_input.peptides.tsv -no_progress -out FileConverter_12.tmp -out_type featureXML > TOPP_FileConverter_12.stdout 2> TOPP_FileConverter_12.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
112 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_12.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
113 FileConverter -test -in FileConverter_13_input.peptides.kroenik -no_progress -out FileConverter_13.tmp -out_type featureXML > TOPP_FileConverter_13.stdout 2> TOPP_FileConverter_13.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
114 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_13.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
115 FileConverter -test -in FileConverter_9_output.featureXML -no_progress -out FileConverter_14.tmp -out_type consensusXML > TOPP_FileConverter_14.stdout 2> TOPP_FileConverter_14.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
116 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_14.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
117 FileConverter -test -in FileConverter_10_input.edta -no_progress -out FileConverter_15.tmp -out_type consensusXML > TOPP_FileConverter_15.stdout 2> TOPP_FileConverter_15.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
118 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_15 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_15.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_15.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
119 FileConverter -test -in FileConverter_16_input.edta -no_progress -out FileConverter_16.tmp -out_type consensusXML > TOPP_FileConverter_16.stdout 2> TOPP_FileConverter_16.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
120 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_16 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_16.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_16.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
121 FileConverter -test -in FileConverter_17_input.consensusXML -no_progress -out FileConverter_17.csv > TOPP_FileConverter_17.stdout 2> TOPP_FileConverter_17.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
122 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_17 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_17.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_17.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
123 FileConverter -test -in FileConverter_17_input.consensusXML -no_progress -out FileConverter_18.tmp -out_type csv > TOPP_FileConverter_18.stdout 2> TOPP_FileConverter_18.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
124 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_18 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_18.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_18.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
125 FileConverter -test -in FileFilter_1_input.mzML -out FileConverter_19.tmp -process_lowmemory -in_type mzML -out_type mzML > TOPP_FileConverter_19.stdout 2> TOPP_FileConverter_19.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
126 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_19 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_19.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_19.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
127 FileConverter -test -in FileConverter_20_input.featureXML -out FileConverter_20.tmp -in_type featureXML -out_type featureXML > TOPP_FileConverter_20.stdout 2> TOPP_FileConverter_20.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
128 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_20 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_20.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_20.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
129 FileConverter -test -in FileConverter_4_input.mzXML -out FileConverter_21.tmp -out_type mzML -process_lowmemory > TOPP_FileConverter_21.stdout 2> TOPP_FileConverter_21.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
130 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_21 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_21.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_21.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
131 FileConverter -test -in FileConverter_23_input.mzML -out FileConverter_23.tmp -out_type mzML > TOPP_FileConverter_23.stdout 2> TOPP_FileConverter_23.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
132 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_23 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_23.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_23.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
133 FileConverter -test -in FileFilter_1_input.mzML -out FileConverter_24.tmp -process_lowmemory -in_type mzML -out_type mzML -lossy_compression -lossy_mass_accuracy 0.0001 > TOPP_FileConverter_24.stdout 2> TOPP_FileConverter_24.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
134 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_24 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_24.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_24.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
135 FileConverter -test -in FileFilter_1_input.mzML -out FileConverter_25.tmp -process_lowmemory -in_type mzML -out_type mzML -lossy_compression > TOPP_FileConverter_25.stdout 2> TOPP_FileConverter_25.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
136 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_25 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_25.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_25.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
137 FileConverter -test -in FileFilter_1_input.mzML -out FileConverter_26.tmp -force_MaxQuant_compatibility -out_type mzXML > TOPP_FileConverter_26.stdout 2> TOPP_FileConverter_26.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
138 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_26 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_26.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_26.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
139 FileConverter -test -in FileConverter_26_output.mzXML -out FileConverter_26-2.tmp -force_MaxQuant_compatibility -out_type mzXML > TOPP_FileConverter_26-2.stdout 2> TOPP_FileConverter_26-2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
140 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_26-2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_26-2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_26-2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
141 FileConverter -test -in FileConverter_27_input.mzML -out FileConverter_27.tmp -out_type mzML -convert_to_chromatograms > TOPP_FileConverter_27.stdout 2> TOPP_FileConverter_27.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
142 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_27 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_27.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_27.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
143 FileConverter -test -in FileConverter_28_input.mzML -out FileConverter_28.tmp -out_type mzML -convert_to_chromatograms > TOPP_FileConverter_28.stdout 2> TOPP_FileConverter_28.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
144 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_28 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_28.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_28.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
145 FileConverter -test -in OpenSwathWorkflow_17_input.mzML -out FileConverter_29.tmp -out_type mzML -lossy_compression -lossy_mass_accuracy 1e-5 -process_lowmemory > TOPP_FileConverter_29.stdout 2> TOPP_FileConverter_29.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
146 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_29 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_29.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_29.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
147 FileConverter -test -in FileConverter_29.tmp -in_type mzML -out FileConverter_29.back.tmp -out_type mzML > TOPP_FileConverter_29_back.stdout 2> TOPP_FileConverter_29_back.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
148 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_29_back failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_29_back.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_29_back.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
149 FileConverter -test -in FileConverter_30_input.mzML -change_im_format multiple -out_type mzML -out FileConverter_30.tmp > TOPP_FileConverter_30.stdout 2> TOPP_FileConverter_30.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
150 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_30 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_30.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_30.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
151 FileConverter -test -in FileConverter_30_output.mzML -change_im_format single -out_type mzML -out FileConverter_31.tmp > TOPP_FileConverter_31.stdout 2> TOPP_FileConverter_31.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
152 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_31 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_31.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_31.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
153 FileFilter -test -in FileFilter_1_input.mzML -out FileFilter_1.tmp -rt :30 -mz :1000 -int :20000 -in_type mzML -out_type mzML > TOPP_FileFilter_1.stdout 2> TOPP_FileFilter_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
154 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
155 FileFilter -test -in FileFilter_1_input.mzML -out FileFilter_2.tmp -rt 30: -mz 1000: -int 100: -in_type mzML -out_type mzML > TOPP_FileFilter_2.stdout 2> TOPP_FileFilter_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
156 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
157 FileFilter -test -in FileFilter_1_input.mzML -out FileFilter_3.tmp -peak_options:level 2 -in_type mzML -out_type mzML > TOPP_FileFilter_3.stdout 2> TOPP_FileFilter_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
158 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
159 FileFilter -test -in FileFilter_4_input.mzML -out FileFilter_4.tmp -spectra:remove_zoom -in_type mzML -out_type mzML > TOPP_FileFilter_4.stdout 2> TOPP_FileFilter_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
160 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
161 FileFilter -test -in FileFilter_5_input.featureXML -out FileFilter_5.tmp -rt :1000 -mz :480 -int :79000 -f_and_c:charge :3 -feature:q :0.6 -in_type featureXML -out_type featureXML > TOPP_FileFilter_5.stdout 2> TOPP_FileFilter_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
162 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
163 FileFilter -test -in FileFilter_5_input.featureXML -out FileFilter_6.tmp -rt 1000: -mz 440: -int 70000: -f_and_c:charge 3: -feature:q 0.51: -in_type featureXML -out_type featureXML > TOPP_FileFilter_6.stdout 2> TOPP_FileFilter_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
164 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
165 FileFilter -test -in FileFilter_7_input.mzML -out FileFilter_7.tmp -int 7000: -peak_options:level 1 2 3 -in_type mzML -out_type mzML > TOPP_FileFilter_7.stdout 2> TOPP_FileFilter_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
166 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
167 FileFilter -test -in FileFilter_8_input.consensusXML -out FileFilter_8.tmp -rt 600:1400 -mz 700:2300 -int 1100:6000 -in_type consensusXML -out_type consensusXML > TOPP_FileFilter_8.stdout 2> TOPP_FileFilter_8.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
168 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_8.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
169 FileFilter -test -in FileFilter_9_input.mzML -out FileFilter_9.tmp -spectra:remove_mode SelectedIonMonitoring -in_type mzML -out_type mzML > TOPP_FileFilter_9.stdout 2> TOPP_FileFilter_9.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
170 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_9.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
171 FileFilter -test -in FileFilter_10_input.mzML -out FileFilter_10.tmp -spectra:remove_activation "Collision-induced dissociation" -in_type mzML -out_type mzML > TOPP_FileFilter_10.stdout 2> TOPP_FileFilter_10.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
172 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_10.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
173 FileFilter -test -in FileFilter_11_input.mzML -out FileFilter_11.tmp -spectra:remove_activation "Plasma desorption" -in_type mzML -out_type mzML > TOPP_FileFilter_11.stdout 2> TOPP_FileFilter_11.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
174 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_11.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
175 FileFilter -test -in FileFilter_12_input.mzML -out FileFilter_12.tmp -peak_options:remove_chromatograms -in_type mzML -out_type mzML > TOPP_FileFilter_12.stdout 2> TOPP_FileFilter_12.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
176 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_12.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
177 FileFilter -test -in FileFilter_13_input.consensusXML -out FileFilter_13.tmp -in_type consensusXML -out_type featureXML -consensus:map 2 > TOPP_FileFilter_13.stdout 2> TOPP_FileFilter_13.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
178 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_13.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
179 FileFilter -test -in FileFilter_14_input.consensusXML -out FileFilter_14.tmp -in_type consensusXML -out_type consensusXML -consensus:map 0 2 > TOPP_FileFilter_14.stdout 2> TOPP_FileFilter_14.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
180 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_14.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
181 FileFilter -test -in FileFilter_15_input.featureXML -out FileFilter_15.tmp -id:sequences_whitelist Oxidation -id:remove_unassigned_ids > TOPP_FileFilter_15.stdout 2> TOPP_FileFilter_15.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
182 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_15 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_15.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_15.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
183 FileFilter -test -in FileFilter_15_input.featureXML -out FileFilter_16.tmp -id:sequences_whitelist Oxidation -id:remove_unassigned_ids -mz 400:600 -rt 3000:4000 > TOPP_FileFilter_16.stdout 2> TOPP_FileFilter_16.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
184 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_16 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_16.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_16.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
185 FileFilter -test -in FileFilter_15_input.featureXML -out FileFilter_17.tmp -id:remove_annotated_features -mz 400:600 -rt 3000:4000 > TOPP_FileFilter_17.stdout 2> TOPP_FileFilter_17.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
186 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_17 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_17.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_17.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
187 FileFilter -test -in FileFilter_18_input.consensusXML -out FileFilter_18.tmp -id:sequences_whitelist Oxidation -id:remove_unassigned_ids > TOPP_FileFilter_18.stdout 2> TOPP_FileFilter_18.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
188 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_18 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_18.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_18.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
189 FileFilter -test -in FileFilter_18_input.consensusXML -out FileFilter_19.tmp -id:remove_unannotated_features -mz 400:600 -rt 3000:4000 > TOPP_FileFilter_19.stdout 2> TOPP_FileFilter_19.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
190 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_19 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_19.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_19.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
191 FileFilter -test -in FileFilter_15_input.featureXML -out FileFilter_20.tmp -id:accessions_whitelist YDL217C -id:remove_unassigned_ids > TOPP_FileFilter_20.stdout 2> TOPP_FileFilter_20.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
192 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_20 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_20.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_20.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
193 FileFilter -test -in FileFilter_15_input.featureXML -out FileFilter_21.tmp -id:remove_unassigned_ids -id:remove_unannotated_features -id:keep_best_score_id > TOPP_FileFilter_21.stdout 2> TOPP_FileFilter_21.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
194 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_21 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_21.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_21.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
195 FileFilter -test -in FileFilter_22_input.consensusXML -out FileFilter_22.tmp -f_and_c:remove_meta distinct_charges gt "1,2" > TOPP_FileFilter_22.stdout 2> TOPP_FileFilter_22.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
196 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_22 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_22.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_22.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
197 FileFilter -test -in FileFilter_22_input.consensusXML -out FileFilter_23.tmp -f_and_c:remove_meta distinct_charges_size gt 2 > TOPP_FileFilter_23.stdout 2> TOPP_FileFilter_23.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
198 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_23 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_23.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_23.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
199 FileFilter -test -in FileFilter_22_input.consensusXML -out FileFilter_24.tmp -f_and_c:remove_meta DOESNOTEXIST lt "whatever" > TOPP_FileFilter_24.stdout 2> TOPP_FileFilter_24.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
200 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_24 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_24.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_24.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
201 FileFilter -test -in FileFilter_25_input.mzML.gz -id:blacklist FileFilter_25_input.idXML -out FileFilter_25.tmp -id:mz 0.05 -id:rt 1 -id:blacklist_imperfect > TOPP_FileFilter_25.stdout 2> TOPP_FileFilter_25.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
202 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_25 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_25.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_25.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
203 FileFilter -test -in FileFilter_25_input.mzML.gz -id:blacklist FileFilter_25_input.idXML -out FileFilter_26.tmp -id:blacklist_imperfect > TOPP_FileFilter_26.stdout 2> TOPP_FileFilter_26.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
204 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_26 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_26.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_26.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
205 FileFilter -test -in FileFilter_28_input.mzML.gz -peak_options:pc_mz_range 832:836 -out FileFilter_28.tmp -peak_options:level 2 > TOPP_FileFilter_28.stdout 2> TOPP_FileFilter_28.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
206 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_28 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_28.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_28.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
207 FileFilter -test -in FileFilter_28_input.mzML.gz -peak_options:pc_mz_range 832:836 -out FileFilter_29.tmp -peak_options:level 1 2 > TOPP_FileFilter_29.stdout 2> TOPP_FileFilter_29.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
208 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_29 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_29.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_29.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
209 FileFilter -test -in FileFilter_28_input.mzML.gz -peak_options:pc_mz_range 832:836 -out FileFilter_30.tmp -peak_options:level 1 2 > TOPP_FileFilter_30.stdout 2> TOPP_FileFilter_30.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
210 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_30 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_30.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_30.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
211 FileFilter -test -in FileFilter_31_34_input.mzML -spectra:remove_isolation_window_width :2 -out FileFilter_31.tmp > TOPP_FileFilter_31.stdout 2> TOPP_FileFilter_31.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
212 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_31 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_31.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_31.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
213 FileFilter -test -in FileFilter_31_34_input.mzML -spectra:select_isolation_window_width :2 -out FileFilter_32.tmp > TOPP_FileFilter_32.stdout 2> TOPP_FileFilter_32.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
214 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_32 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_32.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_32.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
215 FileFilter -test -in FileFilter_31_34_input.mzML -spectra:remove_collision_energy :35 -out FileFilter_33.tmp > TOPP_FileFilter_33.stdout 2> TOPP_FileFilter_33.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
216 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_33 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_33.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_33.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
217 FileFilter -test -in FileFilter_31_34_input.mzML -spectra:select_collision_energy :35 -out FileFilter_34.tmp > TOPP_FileFilter_34.stdout 2> TOPP_FileFilter_34.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
218 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_34 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_34.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_34.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
219 FileFilter -test -in FileFilter_1_input.mzML -out FileFilter_35.tmp -peak_options:indexed_file true -in_type mzML -out_type mzML > TOPP_FileFilter_35.stdout 2> TOPP_FileFilter_35.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
220 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_35 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_35.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_35.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
221 FileFilter -test -in FileFilter_1_input.mzML -out FileFilter_36.tmp -peak_options:indexed_file false -in_type mzML -out_type mzML > TOPP_FileFilter_36.stdout 2> TOPP_FileFilter_36.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
222 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_36 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_36.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_36.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
223 FileFilter -test -in FileFilter_1_input.mzML -out FileFilter_37.tmp -test -peak_options:numpress:intensity slof -peak_options:numpress:masstime linear -in_type mzML -peak_options:numpress:lossy_mass_accuracy 1e-4 -out_type mzML > TOPP_FileFilter_37.stdout 2> TOPP_FileFilter_37.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
224 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_37 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_37.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_37.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
225 FileFilter -test -in FileFilter_1_input.mzML -out FileFilter_38.tmp -test -peak_options:numpress:intensity pic -peak_options:numpress:masstime linear -in_type mzML -peak_options:numpress:lossy_mass_accuracy 1e-4 -out_type mzML > TOPP_FileFilter_38.stdout 2> TOPP_FileFilter_38.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
226 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_38 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_38.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_38.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
227 FileFilter -test -in FileFilter_40_input.mzML -out FileFilter_40.tmp -spectra:select_polarity positive -in_type mzML -out_type mzML > TOPP_FileFilter_40.stdout 2> TOPP_FileFilter_40.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
228 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_40 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_40.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_40.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
229 FileFilter -test -in FileFilter_40_input.mzML -out FileFilter_41.tmp -spectra:select_polarity negative -in_type mzML -out_type mzML > TOPP_FileFilter_41.stdout 2> TOPP_FileFilter_41.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
230 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_41 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_41.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_41.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
231 FileFilter -test -in FileFilter_40_input.mzML -out FileFilter_42.tmp -spectra:select_polarity "" -in_type mzML -out_type mzML > TOPP_FileFilter_42.stdout 2> TOPP_FileFilter_42.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
232 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_42 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_42.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_42.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
233 FileFilter -test -in FileFilter_43_input.mzML -out FileFilter_43.tmp.mzML -in_type mzML -out_type mzML > TOPP_FileFilter_43.stdout 2> TOPP_FileFilter_43.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
234 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_43 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_43.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_43.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
235 FileFilter -test -in FileFilter_43.tmp.mzML -out FileFilter_43.dummy.tmp -in_type mzML -out_type mzML > TOPP_FileFilter_43_read_again.stdout 2> TOPP_FileFilter_43_read_again.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
236 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_43_read_again failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_43_read_again.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_43_read_again.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
237 FileFilter -test -in FileFilter_44_input.mzML -out FileFilter_44.tmp -test -in_type mzML -out_type mzML > TOPP_FileFilter_44.stdout 2> TOPP_FileFilter_44.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
238 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_44 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_44.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_44.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
239 FileFilter -test -in FileFilter_45_input.featureXML -id:sequences_whitelist "YSFS" "STLIPPPSK(Label:13C(6)15N(2))" -out FileFilter_45.tmp > TOPP_FileFilter_45.stdout 2> TOPP_FileFilter_45.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
240 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_45 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_45.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_45.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
241 FileFilter -test -in FileFilter_46_input.featureXML -id:sequences_whitelist "YSFS" "STLIPPPSK(Label:13C(6)15N(2))" -id:sequence_comparison_method "exact" -out FileFilter_46.tmp > TOPP_FileFilter_46.stdout 2> TOPP_FileFilter_46.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
242 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_46 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_46.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_46.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
243 FileFilter -test -in FileFilter_47_input.mzML -spectra:blackorwhitelist:file FileFilter_47_input_select.mzML -spectra:blackorwhitelist:similarity_threshold 0.9 -out FileFilter_47_1.tmp > TOPP_FileFilter_47.stdout 2> TOPP_FileFilter_47.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
244 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_47 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_47.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_47.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
245 FileFilter -test -in FileFilter_47_input.mzML -spectra:blackorwhitelist:file FileFilter_47_input_select.mzML -spectra:blackorwhitelist:similarity_threshold 0.9 -spectra:blackorwhitelist:blacklist false -out FileFilter_48_1.tmp > TOPP_FileFilter_48.stdout 2> TOPP_FileFilter_48.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
246 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_48 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_48.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_48.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
247 FileFilter -test -in FileFilter_49_input.mzML -peak_options:numpress:intensity pic -peak_options:numpress:masstime linear -peak_options:numpress:float_da slof -peak_options:zlib_compression true -out FileFilter_49_1.tmp > TOPP_FileFilter_49.stdout 2> TOPP_FileFilter_49.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
248 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_49 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_49.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_49.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
249 FileInfo -test -in FileInfo_1_input.dta -in_type dta -no_progress -out FileInfo_1.tmp > TOPP_FileInfo_1.stdout 2> TOPP_FileInfo_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
250 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
251 FileInfo -test -in FileInfo_2_input.dta2d -no_progress -out FileInfo_2.tmp > TOPP_FileInfo_2.stdout 2> TOPP_FileInfo_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
252 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
253 FileInfo -test -in FileInfo_3_input.featureXML -m -s -p -no_progress -out FileInfo_3.tmp > TOPP_FileInfo_3.stdout 2> TOPP_FileInfo_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
254 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
255 FileInfo -test -in FileInfo_4_input.mzXML -m -no_progress -out FileInfo_4.tmp > TOPP_FileInfo_4.stdout 2> TOPP_FileInfo_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
256 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
257 FileInfo -test -in FileInfo_5_input.mzDat -in_type mzData -m -s -no_progress -out FileInfo_5.tmp > TOPP_FileInfo_5.stdout 2> TOPP_FileInfo_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
258 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
259 FileInfo -test -in FileInfo_6_input.mzData -d -s -no_progress -out FileInfo_6.tmp > TOPP_FileInfo_6.stdout 2> TOPP_FileInfo_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
260 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
261 FileInfo -test -in FileInfo_7_input.consensusXML -s -m -p -no_progress -out FileInfo_7.tmp > TOPP_FileInfo_7.stdout 2> TOPP_FileInfo_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
262 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
263 FileInfo -test -in FileInfo_9_input.mzML -m -p -s -no_progress -out FileInfo_9.tmp > TOPP_FileInfo_9.stdout 2> TOPP_FileInfo_9.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
264 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_9.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
265 FileInfo -test -in FileInfo_10_input.idXML -no_progress -out FileInfo_10.tmp > TOPP_FileInfo_10.stdout 2> TOPP_FileInfo_10.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
266 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_10.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
267 FileInfo -test -in FileInfo_12_input.mzML -i -no_progress > TOPP_FileInfo_12.stdout 2> TOPP_FileInfo_12.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
268 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_12.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
269 FileInfo -test -in FileInfo_13_input.consensusXML -no_progress > TOPP_FileInfo_13.stdout 2> TOPP_FileInfo_13.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
270 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_13.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
271 FileInfo -test -in FileInfo_14_input.mzid -v -no_progress -out FileInfo_14.tmp > TOPP_FileInfo_14.stdout 2> TOPP_FileInfo_14.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
272 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_14.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
273 FileInfo -test -in FileInfo_15_input.mzid -v -no_progress -out FileInfo_15.tmp > TOPP_FileInfo_15.stdout 2> TOPP_FileInfo_15.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
274 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_15 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_15.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_15.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
275 FileInfo -test -in FileInfo_16_input.trafoXML -out FileInfo_16_output.tmp > TOPP_FileInfo_16.stdout 2> TOPP_FileInfo_16.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
276 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_16 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_16.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_16.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
277 FileInfo -test -in FileInfo_17_input.fasta -out FileInfo_17_output.tmp > TOPP_FileInfo_17.stdout 2> TOPP_FileInfo_17.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
278 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_17 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_17.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_17.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
279 FileInfo -test -in FileInfo_18_input.fasta -out FileInfo_18_output.tmp > TOPP_FileInfo_18.stdout 2> TOPP_FileInfo_18.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
280 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_18 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_18.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_18.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
281 FileMerger -test -in FileMerger_1_input1.dta2d FileMerger_1_input2.dta FileMerger_1_input3.dta2d -out FileMerger_1.tmp -raw:rt_custom 1 2 3 > TOPP_FileMerger_1.stdout 2> TOPP_FileMerger_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
282 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
283 FileMerger -test -in FileMerger_2_input1.dta FileMerger_2_input2.dta -in_type dta -out FileMerger_2.tmp -raw:rt_custom 5 10 > TOPP_FileMerger_2.stdout 2> TOPP_FileMerger_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
284 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
285 FileMerger -test -in FileMerger_3_input1.dta FileMerger_3_input2.dta -out FileMerger_3.tmp -raw:rt_auto > TOPP_FileMerger_3.stdout 2> TOPP_FileMerger_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
286 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
287 FileMerger -test -in FileMerger_4_input1.dta2d FileMerger_4_input2.dta2d -out FileMerger_4.tmp > TOPP_FileMerger_4.stdout 2> TOPP_FileMerger_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
288 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
289 FileMerger -test -in FileMerger_5_input_rt1023.331.dta FileMerger_5_input_rt2044.334.dta FileMerger_5_input_rt889.32.dta -raw:rt_filename -raw:ms_level 2 -out FileMerger_5.tmp > TOPP_FileMerger_5.stdout 2> TOPP_FileMerger_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
290 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
291 FileMerger -test -in FileMerger_6_input1.mzML FileMerger_6_input2.mzML -out FileMerger_6.tmp > TOPP_FileMerger_6.stdout 2> TOPP_FileMerger_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
292 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
293 FileMerger -test -in FileMerger_7_input1.featureXML FileMerger_7_input2.featureXML -out FileMerger_7.tmp > TOPP_FileMerger_7.stdout 2> TOPP_FileMerger_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
294 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
295 FileMerger -test -in FileMerger_8_input1.consensusXML FileMerger_8_input2.consensusXML -out FileMerger_8.tmp > TOPP_FileMerger_8.stdout 2> TOPP_FileMerger_8.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
296 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_8.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
297 FileMerger -test -in FileMerger_9_input1.traML FileMerger_9_input2.traML -out FileMerger_9.tmp > TOPP_FileMerger_9.stdout 2> TOPP_FileMerger_9.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
298 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_9.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
299 FileMerger -test -in FileMerger_6_input2.mzML FileMerger_6_input2.mzML -out FileMerger_10_output.tmp -rt_concat:gap 10.0 -rt_concat:trafo_out FileMerger_10_trafo1.tmp FileMerger_10_trafo2.tmp > TOPP_FileMerger_10.stdout 2> TOPP_FileMerger_10.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
300 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_10.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
301 FileMerger -test -in FileMerger_8_input1.consensusXML FileMerger_8_input2.consensusXML -append_method append_cols -out FileMerger_11.tmp > TOPP_FileMerger_11.stdout 2> TOPP_FileMerger_11.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
302 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_11.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
303 GNPSExport -test -in_cm GNPSExport_single.consensusXML -in_mzml GNPSExport_mz1.mzML -out GNPSExport_1_out.tmp -output_type full_spectra > TOPP_GNPSExport_1.stdout 2> TOPP_GNPSExport_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
304 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_GNPSExport_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_GNPSExport_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_GNPSExport_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
305 GNPSExport -test -in_cm GNPSExport_single.consensusXML -in_mzml GNPSExport_mz1.mzML -out GNPSExport_2_out.tmp -output_type merged_spectra > TOPP_GNPSExport_2.stdout 2> TOPP_GNPSExport_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
306 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_GNPSExport_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_GNPSExport_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_GNPSExport_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
307 GNPSExport -test -in_cm GNPSExport_merged.consensusXML -in_mzml GNPSExport_mz1.mzML GNPSExport_mz2.mzML -out GNPSExport_3_out.tmp -output_type full_spectra > TOPP_GNPSExport_3.stdout 2> TOPP_GNPSExport_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
308 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_GNPSExport_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_GNPSExport_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_GNPSExport_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
309 GNPSExport -test -in_cm GNPSExport_merged.consensusXML -in_mzml GNPSExport_mz1.mzML GNPSExport_mz2.mzML -out GNPSExport_4_out.tmp > TOPP_GNPSExport_4.stdout 2> TOPP_GNPSExport_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
310 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_GNPSExport_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_GNPSExport_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_GNPSExport_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
311 HighResPrecursorMassCorrector -test -in HighResPrecursorMassCorrector_2860_1103_3.mzML -feature:in HighResPrecursorMassCorrector_2860_1103_3.featureXML -out HighResPrecursorMassCorrector_2860_1103_3_out.tmp > TOPP_HighResPrecursorMassCorrector_1.stdout 2> TOPP_HighResPrecursorMassCorrector_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
312 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_HighResPrecursorMassCorrector_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_HighResPrecursorMassCorrector_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_HighResPrecursorMassCorrector_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
313 HighResPrecursorMassCorrector -test -in HighResPrecursorMassCorrector_1035_1178_4.mzML -feature:in HighResPrecursorMassCorrector_1035_1178_4.featureXML -feature:max_trace 4 -feature:mz_tolerance 10 -out HighResPrecursorMassCorrector_1035_1178_4_out.tmp > TOPP_HighResPrecursorMassCorrector_2.stdout 2> TOPP_HighResPrecursorMassCorrector_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
314 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_HighResPrecursorMassCorrector_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_HighResPrecursorMassCorrector_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_HighResPrecursorMassCorrector_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
315 HighResPrecursorMassCorrector -test -in HighResPrecursorMassCorrector_2538_1091_2.mzML -feature:in HighResPrecursorMassCorrector_2538_1091_2.featureXML -out HighResPrecursorMassCorrector_2538_1091_2_out.tmp > TOPP_HighResPrecursorMassCorrector_3.stdout 2> TOPP_HighResPrecursorMassCorrector_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
316 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_HighResPrecursorMassCorrector_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_HighResPrecursorMassCorrector_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_HighResPrecursorMassCorrector_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
317 HighResPrecursorMassCorrector -test -in HighResPrecursorMassCorrector_2810_1091_3.mzML -feature:in HighResPrecursorMassCorrector_2810_1091_3.featureXML -out HighResPrecursorMassCorrector_2810_1091_3_out.tmp > TOPP_HighResPrecursorMassCorrector_4.stdout 2> TOPP_HighResPrecursorMassCorrector_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
318 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_HighResPrecursorMassCorrector_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_HighResPrecursorMassCorrector_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_HighResPrecursorMassCorrector_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
319 HighResPrecursorMassCorrector -test -in HighResPrecursorMassCorrector_3070_1191_3.mzML -feature:in HighResPrecursorMassCorrector_3070_1191_3.featureXML -out HighResPrecursorMassCorrector_3070_1191_3_out.tmp > TOPP_HighResPrecursorMassCorrector_5.stdout 2> TOPP_HighResPrecursorMassCorrector_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
320 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_HighResPrecursorMassCorrector_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_HighResPrecursorMassCorrector_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_HighResPrecursorMassCorrector_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
321 HighResPrecursorMassCorrector -test -in HighResPrecursorMassCorrector_6.mzML -highest_intensity_peak:mz_tolerance 0.2 -out HighResPrecursorMassCorrector_6_out.tmp > TOPP_HighResPrecursorMassCorrector_6.stdout 2> TOPP_HighResPrecursorMassCorrector_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
322 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_HighResPrecursorMassCorrector_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_HighResPrecursorMassCorrector_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_HighResPrecursorMassCorrector_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
323 IDRTCalibration -test -in IDRTCalibration_1_input.idXML -out IDRTCalibration_1_output.tmp -calibrant_1_input 10 -calibrant_2_input 90 > TOPP_IDRTCalibration_1.stdout 2> TOPP_IDRTCalibration_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
324 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDRTCalibration_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDRTCalibration_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDRTCalibration_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
325 IDRTCalibration -test -in degenerated_empty.idXML -out IDRTCalibration_2_output.tmp -calibrant_1_input 10 -calibrant_2_input 90 > TOPP_IDRTCalibration_2.stdout 2> TOPP_IDRTCalibration_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
326 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDRTCalibration_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDRTCalibration_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDRTCalibration_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
327 IDMassAccuracy -test -in spectra.mzML -id_in MSGFPlusAdapter_1_out.idXML -number_of_bins 10 -out_fragment IDMassAccuracy_1_out_fragment.tsv -out_fragment_fit IDMassAccuracy_1_out_fragment_fit.tsv -out_precursor IDMassAccuracy_1_out_precursor.tsv -out_precursor_fit IDMassAccuracy_1_out_precursor_fit.tsv > TOPP_IDMassAccuracy_1.stdout 2> TOPP_IDMassAccuracy_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
328 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMassAccuracy_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMassAccuracy_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMassAccuracy_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
329 IsobaricAnalyzer -test -in IsobaricAnalyzer_input_1.mzML -ini IsobaricAnalyzer.ini -out IsobaricAnalyzer_output_1.tmp > TOPP_IsobaricAnalyzer_1.stdout 2> TOPP_IsobaricAnalyzer_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
330 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IsobaricAnalyzer_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IsobaricAnalyzer_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IsobaricAnalyzer_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
331 IsobaricAnalyzer -test -in TMTTenPlexMethod_test.mzML -ini TMTTenPlexMethod_test.ini -out TMTTenPlexMethod_output.tmp > TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1.stdout 2> TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
332 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
333 IsobaricAnalyzer -test -in TMTTenPlexMethod_test.mzML -ini TMTElevenPlexMethod_test.ini -out TMTElevenPlexMethod_output.tmp > TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1.stdout 2> TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
334 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
335 IsobaricAnalyzer -test -in MS3_nonHierarchical.mzML -extraction:select_activation "Collision-induced dissociation" -type tmt10plex -out MS3TMT10Plex_output.tmp > TOPP_IsobaricAnalyzer_MS3TMT10Plex_1.stdout 2> TOPP_IsobaricAnalyzer_MS3TMT10Plex_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
336 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IsobaricAnalyzer_MS3TMT10Plex_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IsobaricAnalyzer_MS3TMT10Plex_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IsobaricAnalyzer_MS3TMT10Plex_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
337 IDConflictResolver -test -in IDConflictResolver_1_input.featureXML -out IDConflictResolver_1_output.tmp > TOPP_IDConflictResolver_1.stdout 2> TOPP_IDConflictResolver_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
338 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDConflictResolver_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDConflictResolver_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDConflictResolver_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
339 IDConflictResolver -test -in IDConflictResolver_2_input.consensusXML -out IDConflictResolver_2_output.tmp > TOPP_IDConflictResolver_2.stdout 2> TOPP_IDConflictResolver_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
340 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDConflictResolver_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDConflictResolver_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDConflictResolver_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
341 IDConflictResolver -test -in IDConflictResolver_3_input.consensusXML -out IDConflictResolver_3_output.tmp > TOPP_IDConflictResolver_3.stdout 2> TOPP_IDConflictResolver_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
342 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDConflictResolver_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDConflictResolver_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDConflictResolver_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
343 IDConflictResolver -test -in IDConflictResolver_4_input.featureXML -resolve_between_features highest_intensity -out IDConflictResolver_4.tmp > TOPP_IDConflictResolver_4.stdout 2> TOPP_IDConflictResolver_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
344 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDConflictResolver_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDConflictResolver_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDConflictResolver_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
345 IDFileConverter -test -in IDFileConverter_1_input1.mascotXML -mz_file IDFileConverter_1_input2.mzML -out IDFileConverter_1_output.tmp -out_type idXML > TOPP_IDFileConverter_1.stdout 2> TOPP_IDFileConverter_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
346 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
347 IDFileConverter -test -in PepXMLFile_test.pepxml -mz_file PepXMLFile_test.mzML -mz_name PepXMLFile_test -out IDFileConverter_2_output.tmp -out_type idXML > TOPP_IDFileConverter_2.stdout 2> TOPP_IDFileConverter_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
348 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
349 IDFileConverter -test -in IDFileConverter_3_input.protXML -out IDFileConverter_3_output.tmp -out_type idXML > TOPP_IDFileConverter_3.stdout 2> TOPP_IDFileConverter_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
350 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
351 IDFileConverter -test -in IDFileConverter_1_input1.mascotXML -mz_file IDFileConverter_1_input2.mzML -out IDFileConverter_5_output.tmp -ini IDFileConverter_5_parameters.ini > TOPP_IDFileConverter_5.stdout 2> TOPP_IDFileConverter_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
352 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
353 IDFileConverter -test -in IDFileConverter_6_input1.pepXML -mz_file IDFileConverter_1_input2.mzML -mz_name F025589.dat.mzML -out IDFileConverter_6_output.tmp -out_type idXML > TOPP_IDFileConverter_6.stdout 2> TOPP_IDFileConverter_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
354 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
355 IDFileConverter -test -in IDFileConverter_7_input1.xml -out IDFileConverter_7_output.tmp -out_type idXML > TOPP_IDFileConverter_7.stdout 2> TOPP_IDFileConverter_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
356 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
357 IDFileConverter -test -in IDFileConverter_8_input.mzid -out IDFileConverter_8_output.tmp -out_type idXML > TOPP_IDFileConverter_8.stdout 2> TOPP_IDFileConverter_8.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
358 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_8.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
359 IDFileConverter -test -in IDFileConverter_9_input.idXML -out IDFileConverter_9_output.tmp -out_type mzid > TOPP_IDFileConverter_9.stdout 2> TOPP_IDFileConverter_9.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
360 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_9.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
361 IDFileConverter -test -in IDFileConverter_10_input.pepXML -out IDFileConverter_10_output.tmp -out_type idXML > TOPP_IDFileConverter_10.stdout 2> TOPP_IDFileConverter_10.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
362 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_10.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
363 IDFileConverter -test -in IDFileConverter_11_input.tsv -out IDFileConverter_11_output.tmp -out_type idXML > TOPP_IDFileConverter_11.stdout 2> TOPP_IDFileConverter_11.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
364 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_11.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
365 IDFileConverter -test -in IDFileConverter_12_input.psms -out IDFileConverter_12_output.tmp -out_type idXML -score_type qvalue > TOPP_IDFileConverter_12.stdout 2> TOPP_IDFileConverter_12.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
366 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_12.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
367 IDFileConverter -test -in IDFileConverter_12_input.psms -out IDFileConverter_13_output.tmp -out_type idXML -score_type PEP > TOPP_IDFileConverter_13.stdout 2> TOPP_IDFileConverter_13.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
368 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_13.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
369 IDFileConverter -test -in IDFileConverter_12_input.psms -out IDFileConverter_14_output.tmp -out_type idXML -score_type score > TOPP_IDFileConverter_14.stdout 2> TOPP_IDFileConverter_14.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
370 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_14.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
371 IDFileConverter -test -in MSGFPlusAdapter_1_out.mzid -out IDFileConverter_15_output.tmp -out_type idXML -mz_file spectra.mzML > TOPP_IDFileConverter_15.stdout 2> TOPP_IDFileConverter_15.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
372 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_15 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_15.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_15.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
373 IDFileConverter -test -in IDFileConverter_16_input.pepXML -out IDFileConverter_16_output.tmp -out_type idXML > TOPP_IDFileConverter_16.stdout 2> TOPP_IDFileConverter_16.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
374 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_16 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_16.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_16.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
375 IDFileConverter -test -in IDFileConverter_17_input.idXML -out IDFileConverter_17_output.tmp -out_type pepXML > TOPP_IDFileConverter_17.stdout 2> TOPP_IDFileConverter_17.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
376 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_17 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_17.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_17.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
377 IDFileConverter -test -in IDFileConverter_18_input.idXML -out IDFileConverter_18_output.tmp -out_type pepXML > TOPP_IDFileConverter_18.stdout 2> TOPP_IDFileConverter_18.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
378 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_18 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_18.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_18.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
379 IDFileConverter -test -in IDFileConverter_19_input.idXML -out IDFileConverter_19_output.tmp -out_type pepXML > TOPP_IDFileConverter_19.stdout 2> TOPP_IDFileConverter_19.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
380 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_19 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_19.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_19.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
381 IDFileConverter -test -in IDFileConverter_20_input.idXML -out IDFileConverter_20_output.tmp -out_type pepXML > TOPP_IDFileConverter_20.stdout 2> TOPP_IDFileConverter_20.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
382 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_20 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_20.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_20.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
383 IDFileConverter -test -in IDFileConverter_21_input.idXML -out_type idXML -out IDFileConverter_21_output.tmp -mz_file IDMapper_4_input.mzML > TOPP_IDFileConverter_21.stdout 2> TOPP_IDFileConverter_21.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
384 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_21 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_21.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_21.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
385 IDFileConverter -test -in MSGFPlusAdapter_1_out.mzid -out IDFileConverter_22_output.tmp -out_type idXML -mz_file spectra.mzML -add_ionmatch_annotation 0.01 > TOPP_IDFileConverter_22.stdout 2> TOPP_IDFileConverter_22.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
386 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_22 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_22.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_22.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
387 IDFileConverter -test -in IDFileConverter_23_input.mzid -out IDFileConverter_23_output.tmp -out_type idXML > TOPP_IDFileConverter_23.stdout 2> TOPP_IDFileConverter_23.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
388 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_23 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_23.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_23.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
389 IDFileConverter -test -in IDFileConverter_24_input.pep.xml -out IDFileConverter_24_output.tmp -out_type idXML > TOPP_IDFileConverter_24.stdout 2> TOPP_IDFileConverter_24.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
390 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_24 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_24.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_24.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
391 IDFileConverter -test -in IDFileConverter_25_input.idXML -out IDFileConverter_25_output.tmp -out_type pepXML > TOPP_IDFileConverter_25.stdout 2> TOPP_IDFileConverter_25.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
392 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_25 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_25.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_25.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
393 IDFileConverter -test -in IDFileConverter_26_input.mzid -out IDFileConverter_26_output.tmp -out_type idXML > TOPP_IDFileConverter_26.stdout 2> TOPP_IDFileConverter_26.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
394 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_26 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_26.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_26.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
395 IDFilter -test -in IDFilter_1_input.idXML -out IDFilter_1_output.tmp -whitelist:proteins IDFilter_1_input.fas > TOPP_IDFilter_1.stdout 2> TOPP_IDFilter_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
396 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
397 IDFilter -test -in IDFilter_3_input.idXML -out IDFilter_3_output.tmp -blacklist:peptides IDFilter_3_2_input.idXML > TOPP_IDFilter_3.stdout 2> TOPP_IDFilter_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
398 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
399 IDFilter -test -in IDFilter_4_input.idXML -out IDFilter_4_output.tmp -rt:p_value 0.08 > TOPP_IDFilter_4.stdout 2> TOPP_IDFilter_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
400 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
401 IDFilter -test -in IDFilter_5_input.idXML -out IDFilter_5_output.tmp -score:pep 32 -score:prot 25 > TOPP_IDFilter_5.stdout 2> TOPP_IDFilter_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
402 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
403 IDFilter -test -in IDFilter_5_input.idXML -out IDFilter_5a_output.tmp -score:pep 32 > TOPP_IDFilter_5a.stdout 2> TOPP_IDFilter_5a.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
404 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_5a failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_5a.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_5a.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
405 IDFilter -test -in IDFilter_5_input.idXML -out IDFilter_5b_output.tmp -score:prot 25 > TOPP_IDFilter_5b.stdout 2> TOPP_IDFilter_5b.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
406 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_5b failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_5b.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_5b.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
407 IDFilter -test -in IDFilter_5_input.idXML -out IDFilter_5c_output.tmp -score:prot 25 -delete_unreferenced_peptide_hits > TOPP_IDFilter_5c.stdout 2> TOPP_IDFilter_5c.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
408 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_5c failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_5c.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_5c.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
409 IDFilter -test -in IDFilter_6_input.idXML -out IDFilter_6_output.tmp -best:n_peptide_hits 2 -best:n_protein_hits 10 > TOPP_IDFilter_6.stdout 2> TOPP_IDFilter_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
410 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
411 IDFilter -test -in IDFilter_7_input.idXML -out IDFilter_7_output.tmp -remove_duplicate_psm > TOPP_IDFilter_7.stdout 2> TOPP_IDFilter_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
412 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
413 IDFilter -test -in IDFilter_8_input.idXML -out IDFilter_8_output.tmp -precursor:rt 200:350 -precursor:mz 999:1000 > TOPP_IDFilter_8.stdout 2> TOPP_IDFilter_8.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
414 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_8.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
415 IDFilter -test -in IDFilter_9_input.idXML -out IDFilter_9_output.tmp -score:pep 0.05 > TOPP_IDFilter_9.stdout 2> TOPP_IDFilter_9.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
416 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_9.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
417 IDFilter -test -in IDFilter_10_input.idXML -out IDFilter_10_output.tmp -score:prot 0.3 -delete_unreferenced_peptide_hits > TOPP_IDFilter_10.stdout 2> TOPP_IDFilter_10.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
418 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_10.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
419 IDFilter -test -in IDFilter_11_input.idXML -out IDFilter_11_output.tmp -remove_decoys -delete_unreferenced_peptide_hits > TOPP_IDFilter_11.stdout 2> TOPP_IDFilter_11.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
420 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_11.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
421 IDFilter -test -in IDFilter_12_input.idXML -out IDFilter_12_output.tmp -in_silico_digestion:fasta IDFilter_12_input.fasta > TOPP_IDFilter_12.stdout 2> TOPP_IDFilter_12.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
422 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_12.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
423 IDFilter -test -in IDFilter_13_input.idXML -out IDFilter_13_output.tmp -in_silico_digestion:fasta IDFilter_13_input.fasta -in_silico_digestion:missed_cleavages 1 > TOPP_IDFilter_13.stdout 2> TOPP_IDFilter_13.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
424 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_13.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
425 IDFilter -test -in IDFilter_14_input.idXML -out IDFilter_14_output.tmp -in_silico_digestion:fasta IDFilter_14_input.fasta -in_silico_digestion:enzyme Trypsin/P -in_silico_digestion:missed_cleavages 1 > TOPP_IDFilter_14.stdout 2> TOPP_IDFilter_14.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
426 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_14.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
427 IDFilter -test -in IDFilter_15_input.idXML -out IDFilter_15_output.tmp -in_silico_digestion:fasta IDFilter_15_input.fasta -in_silico_digestion:enzyme Trypsin/P -in_silico_digestion:missed_cleavages 1 -in_silico_digestion:specificity semi > TOPP_IDFilter_15.stdout 2> TOPP_IDFilter_15.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
428 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_15 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_15.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_15.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
429 IDFilter -test -in IDFilter_16_input.idXML -out IDFilter_16_output.tmp -in_silico_digestion:fasta IDFilter_16_input.fasta -in_silico_digestion:enzyme Trypsin/P -in_silico_digestion:missed_cleavages 1 -in_silico_digestion:methionine_cleavage > TOPP_IDFilter_16.stdout 2> TOPP_IDFilter_16.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
430 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_16 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_16.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_16.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
431 IDFilter -test -in IDFilter_missed_cleavages_input.idXML -out IDFilter_17_output.tmp -missed_cleavages:enzyme Lys-N -missed_cleavages:number_of_missed_cleavages :2 > TOPP_IDFilter_17.stdout 2> TOPP_IDFilter_17.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
432 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_17 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_17.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_17.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
433 IDFilter -test -in IDFilter_missed_cleavages_input.idXML -out IDFilter_18_output.tmp -missed_cleavages:enzyme Lys-N -missed_cleavages:number_of_missed_cleavages 2: > TOPP_IDFilter_18.stdout 2> TOPP_IDFilter_18.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
434 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_18 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_18.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_18.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
435 IDFilter -test -in IDFilter_missed_cleavages_input.idXML -out IDFilter_19_output.tmp -missed_cleavages:enzyme Lys-N -missed_cleavages:number_of_missed_cleavages 1:3 > TOPP_IDFilter_19.stdout 2> TOPP_IDFilter_19.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
436 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_19 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_19.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_19.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
437 IDFilter -test -in IDFilter_missed_cleavages_input.idXML -out IDFilter_20_output.tmp -missed_cleavages:number_of_missed_cleavages 1:0 > TOPP_IDFilter_20.stdout 2> TOPP_IDFilter_20.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
438 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_20 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_20.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_20.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
439 IDFilter -test -in IDFilter_16_input.idXML -out IDFilter_21_output.tmp -remove_peptide_hits_by_metavalue "calcMZ" "gt" "750.0" > TOPP_IDFilter_21.stdout 2> TOPP_IDFilter_21.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
440 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_21 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_21.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_21.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
441 IDFilter -test -in IDFilter_16_input.idXML -out IDFilter_22_output.tmp -remove_peptide_hits_by_metavalue "end" "ne" "23" > TOPP_IDFilter_22.stdout 2> TOPP_IDFilter_22.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
442 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_22 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_22.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_22.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
443 MapAlignerPoseClustering -test -ini MapAlignerPoseClustering_1_parameters.ini -in MapAlignerPoseClustering_1_input1.featureXML MapAlignerPoseClustering_1_input2.featureXML MapAlignerPoseClustering_1_input3.featureXML -out MapAlignerPoseClustering_1_output1.tmp MapAlignerPoseClustering_1_output2.tmp MapAlignerPoseClustering_1_output3.tmp -trafo_out MapAlignerPoseClustering_1_trafo1.tmp MapAlignerPoseClustering_1_trafo2.tmp MapAlignerPoseClustering_1_trafo3.tmp > TOPP_MapAlignerPoseClustering_1.stdout 2> TOPP_MapAlignerPoseClustering_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
444 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerPoseClustering_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerPoseClustering_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerPoseClustering_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
445 MapAlignerPoseClustering -test -ini MapAlignerPoseClustering_2_parameters.ini -in MapAlignerPoseClustering_2_input1.mzML MapAlignerPoseClustering_2_input2.mzML MapAlignerPoseClustering_2_input3.mzML -out MapAlignerPoseClustering_2_output1.tmp MapAlignerPoseClustering_2_output2.tmp MapAlignerPoseClustering_2_output3.tmp > TOPP_MapAlignerPoseClustering_2.stdout 2> TOPP_MapAlignerPoseClustering_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
446 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerPoseClustering_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerPoseClustering_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerPoseClustering_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
447 MapAlignerPoseClustering -test -ini MapAlignerPoseClustering_1_parameters.ini -in MapAlignerPoseClustering_1_input2.featureXML MapAlignerPoseClustering_1_input3.featureXML -out MapAlignerPoseClustering_3_output1.tmp MapAlignerPoseClustering_3_output2.tmp -reference:file MapAlignerPoseClustering_1_input1.featureXML > TOPP_MapAlignerPoseClustering_3.stdout 2> TOPP_MapAlignerPoseClustering_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
448 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerPoseClustering_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerPoseClustering_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerPoseClustering_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
449 MapAlignerPoseClustering -test -ini MapAlignerPoseClustering_1_parameters.ini -in MapAlignerPoseClustering_1_input1.featureXML MapAlignerPoseClustering_1_input2.featureXML -trafo_out MapAlignerPoseClustering_4_trafo1.tmp MapAlignerPoseClustering_4_trafo2.tmp -reference:index 2 > TOPP_MapAlignerPoseClustering_4.stdout 2> TOPP_MapAlignerPoseClustering_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
450 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerPoseClustering_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerPoseClustering_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerPoseClustering_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
451 MapAlignerIdentification -test -ini MapAlignerIdentification_parameters.ini -in MapAlignerIdentification_1_input1.featureXML MapAlignerIdentification_1_input2.featureXML -out MapAlignerIdentification_1_output1.tmp MapAlignerIdentification_1_output2.tmp > TOPP_MapAlignerIdentification_1.stdout 2> TOPP_MapAlignerIdentification_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
452 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerIdentification_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerIdentification_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerIdentification_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
453 MapAlignerIdentification -test -ini MapAlignerIdentification_parameters.ini -in MapAlignerIdentification_1_input1.featureXML -out MapAlignerIdentification_2_output1.tmp -reference:file MapAlignerIdentification_1_input2.featureXML > TOPP_MapAlignerIdentification_2.stdout 2> TOPP_MapAlignerIdentification_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
454 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerIdentification_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerIdentification_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerIdentification_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
455 MapAlignerIdentification -test -ini MapAlignerIdentification_parameters.ini -in MapAlignerIdentification_1_input2.featureXML MapAlignerIdentification_1_input1.featureXML -out MapAlignerIdentification_3_output1.tmp MapAlignerIdentification_3_output2.tmp -reference:index 1 > TOPP_MapAlignerIdentification_3.stdout 2> TOPP_MapAlignerIdentification_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
456 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerIdentification_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerIdentification_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerIdentification_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
457 MapAlignerIdentification -test -ini MapAlignerIdentification_parameters.ini -in MapAlignerIdentification_1_input1.featureXML MapAlignerIdentification_1_input2.featureXML -out MapAlignerIdentification_4_output1.tmp MapAlignerIdentification_4_output2.tmp -reference:index 2 > TOPP_MapAlignerIdentification_4.stdout 2> TOPP_MapAlignerIdentification_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
458 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerIdentification_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerIdentification_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerIdentification_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
459 MapAlignerIdentification -test -ini MapAlignerIdentification_parameters.ini -in MapAlignerIdentification_5_input1.consensusXML MapAlignerIdentification_5_input2.consensusXML -out MapAlignerIdentification_5_output1.tmp MapAlignerIdentification_5_output2.tmp > TOPP_MapAlignerIdentification_5.stdout 2> TOPP_MapAlignerIdentification_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
460 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerIdentification_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerIdentification_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerIdentification_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
461 MapAlignerIdentification -test -ini MapAlignerIdentification_parameters.ini -in MapAlignerIdentification_1_input1.featureXML -trafo_out MapAlignerIdentification_6_output1.tmp -reference:file MapAlignerIdentification_1_input2.featureXML > TOPP_MapAlignerIdentification_6.stdout 2> TOPP_MapAlignerIdentification_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
462 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerIdentification_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerIdentification_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerIdentification_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
463 MapAlignerSpectrum -test -ini MapAlignerSpectrum_parameters.ini -in MapAlignerSpectrum_1_input1.mzML MapAlignerSpectrum_1_input2.mzML MapAlignerSpectrum_1_input3.mzML -out MapAlignerSpectrum_1_output1.tmp MapAlignerSpectrum_1_output2.tmp MapAlignerSpectrum_1_output3.tmp > TOPP_MapAlignerSpectrum_1.stdout 2> TOPP_MapAlignerSpectrum_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
464 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerSpectrum_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerSpectrum_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerSpectrum_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
465 MapAlignerTreeGuided -test -ini MapAlignerTreeGuided_parameters.ini -in MapAlignerTreeGuided_1_input1.featureXML MapAlignerTreeGuided_1_input2.featureXML MapAlignerTreeGuided_1_input3.featureXML -out MapAlignerTreeGuided_1_output1.tmp MapAlignerTreeGuided_1_output2.tmp MapAlignerTreeGuided_1_output3.tmp > TOPP_MapAlignerTreeGuided_1.stdout 2> TOPP_MapAlignerTreeGuided_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
466 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerTreeGuided_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerTreeGuided_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerTreeGuided_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
467 MapAlignerTreeGuided -test -ini MapAlignerTreeGuided_parameters.ini -in MapAlignerTreeGuided_1_input1.featureXML MapAlignerTreeGuided_1_input2.featureXML MapAlignerTreeGuided_1_input3.featureXML -trafo_out MapAlignerTreeGuided_2_output1.tmp MapAlignerTreeGuided_2_output2.tmp MapAlignerTreeGuided_2_output3.tmp > TOPP_MapAlignerTreeGuided_2.stdout 2> TOPP_MapAlignerTreeGuided_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
468 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerTreeGuided_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerTreeGuided_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerTreeGuided_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
469 MapRTTransformer -test -in MapRTTransformer_1_input.featureXML -trafo_in MapRTTransformer_trafo_linear.trafoXML -out MapRTTransformer_1_output.tmp > TOPP_MapRTTransformer_1.stdout 2> TOPP_MapRTTransformer_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
470 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapRTTransformer_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapRTTransformer_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapRTTransformer_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
471 MapRTTransformer -test -in MapRTTransformer_2_input.mzML -trafo_in MapRTTransformer_trafo_linear.trafoXML -out MapRTTransformer_2_output.tmp > TOPP_MapRTTransformer_2.stdout 2> TOPP_MapRTTransformer_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
472 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapRTTransformer_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapRTTransformer_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapRTTransformer_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
473 MapRTTransformer -test -invert -trafo_in MapAlignerPoseClustering_1_trafo2.trafoXML -trafo_out MapRTTransformer_3_output.tmp > TOPP_MapRTTransformer_3.stdout 2> TOPP_MapRTTransformer_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
474 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapRTTransformer_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapRTTransformer_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapRTTransformer_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
475 MapRTTransformer -test -in MapRTTransformer_4_input.chrom.mzML -trafo_in MapRTTransformer_trafo_linear.trafoXML -out MapRTTransformer_4_output.tmp > TOPP_MapRTTransformer_4.stdout 2> TOPP_MapRTTransformer_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
476 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapRTTransformer_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapRTTransformer_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapRTTransformer_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
477 MapRTTransformer -test -in MapRTTransformer_1_input.featureXML -trafo_in MapRTTransformer_trafo_none.trafoXML -out MapRTTransformer_5_output.tmp > TOPP_MapRTTransformer_5.stdout 2> TOPP_MapRTTransformer_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
478 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapRTTransformer_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapRTTransformer_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapRTTransformer_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
479 MapRTTransformer -test -in MapRTTransformer_1_input.featureXML -trafo_in MapRTTransformer_trafo_linear.trafoXML -out MapRTTransformer_6_output.tmp -store_original_rt > TOPP_MapRTTransformer_6.stdout 2> TOPP_MapRTTransformer_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
480 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapRTTransformer_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapRTTransformer_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapRTTransformer_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
481 MetaProSIP -test -in_mzML MetaProSIP_1_input.mzML -in_fasta MetaProSIP_1_input.fasta -in_featureXML MetaProSIP_1_input.featureXML -out_csv MetaProSIP_1_output_1.tmp -out_peptide_centric_csv MetaProSIP_1_output_2.tmp > TOPP_MetaProSIP_1.stdout 2> TOPP_MetaProSIP_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
482 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MetaProSIP_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MetaProSIP_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MetaProSIP_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
483 MascotAdapter -test -ini MascotAdapter_1_parameters.ini -mascot_in -in MascotAdapter_1_input.mzData > TOPP_MascotAdapter_1.stdout 2> TOPP_MascotAdapter_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
484 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MascotAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MascotAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MascotAdapter_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
485 MascotAdapter -test -in MascotAdapter_2_input.mascotXML -out MascotAdapter_2_output.tmp -mascot_out > TOPP_MascotAdapter_2.stdout 2> TOPP_MascotAdapter_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
486 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MascotAdapter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MascotAdapter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MascotAdapter_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
487 MSstatsConverter -test -in MSstatsConverter_1_in.consensusXML -retention_time_summarization_method max -in_design MSstatsConverter_1_design.tsv -out MSstatsConverter_1_out.tmp > TOPP_MSstatsConverter_1.stdout 2> TOPP_MSstatsConverter_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
488 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MSstatsConverter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MSstatsConverter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MSstatsConverter_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
489 MSstatsConverter -test -in MSstatsConverter_2_in.consensusXML -method "ISO" -retention_time_summarization_method manual -in_design MSstatsConverter_2_design.tsv -out MSstatsConverter_2_out.tmp -msstats_bioreplicate MSstats_BioReplicate -msstats_condition MSstats_Condition -msstats_mixture MSstats_Mixture > TOPP_MSstatsConverter_2.stdout 2> TOPP_MSstatsConverter_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
490 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MSstatsConverter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MSstatsConverter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MSstatsConverter_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
491 MSstatsConverter -test -in MSstatsConverter_3_in.consensusXML -method "ISO" -retention_time_summarization_method manual -in_design MSstatsConverter_3_design.tsv -out MSstatsConverter_3_out.tmp -msstats_bioreplicate MSstats_BioReplicate -msstats_condition MSstats_Condition -msstats_mixture MSstats_Mixture > TOPP_MSstatsConverter_3.stdout 2> TOPP_MSstatsConverter_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
492 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MSstatsConverter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MSstatsConverter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MSstatsConverter_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
493 SpecLibSearcher -test -ini SpecLibSearcher_1_parameters.ini -in SpecLibSearcher_1.mzML -lib SpecLibSearcher_1.MSP -out SpecLibSearcher_1.tmp > TOPP_SpecLibSearcher_1.stdout 2> TOPP_SpecLibSearcher_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
494 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SpecLibSearcher_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SpecLibSearcher_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SpecLibSearcher_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
495 OpenSwathAssayGenerator -test -in OpenSwathAssayGenerator_input.TraML -out OpenSwathAssayGenerator_output.TraML.tmp -out_type TraML -min_transitions 6 -max_transitions 6 -allowed_fragment_types b,y -allowed_fragment_charges 2,3 -enable_detection_specific_losses > TOPP_OpenSwathAssayGenerator_test_1.stdout 2> TOPP_OpenSwathAssayGenerator_test_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
496 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAssayGenerator_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAssayGenerator_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAssayGenerator_test_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
497 OpenSwathAssayGenerator -test -in OpenSwathAssayGenerator_input_2.TraML -out OpenSwathAssayGenerator_output_2.TraML.tmp -out_type TraML -allowed_fragment_charges 1,2,3,4 -enable_ipf -unimod_file OpenSwathAssayGenerator_input_2_unimod.xml > TOPP_OpenSwathAssayGenerator_test_2.stdout 2> TOPP_OpenSwathAssayGenerator_test_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
498 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAssayGenerator_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAssayGenerator_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAssayGenerator_test_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
499 OpenSwathAssayGenerator -test -in OpenSwathAssayGenerator_input_2.TraML -out OpenSwathAssayGenerator_output_3.TraML.tmp -out_type TraML -allowed_fragment_charges 1,2,3,4 -enable_ipf -unimod_file OpenSwathAssayGenerator_input_3_unimod.xml > TOPP_OpenSwathAssayGenerator_test_3.stdout 2> TOPP_OpenSwathAssayGenerator_test_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
500 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAssayGenerator_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAssayGenerator_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAssayGenerator_test_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
501 OpenSwathDecoyGenerator -test -in OpenSwathDecoyGenerator_input.TraML -out OpenSwathDecoyGenerator.TraML.tmp -out_type TraML -method pseudo-reverse -separate -switchKR false > TOPP_OpenSwathDecoyGenerator_test_1.stdout 2> TOPP_OpenSwathDecoyGenerator_test_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
502 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathDecoyGenerator_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathDecoyGenerator_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathDecoyGenerator_test_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
503 OpenSwathDecoyGenerator -test -in OpenSwathDecoyGenerator_input_2.TraML -out OpenSwathDecoyGenerator_2.TraML.tmp -out_type TraML -method pseudo-reverse -product_mz_threshold 0.8 -switchKR false > TOPP_OpenSwathDecoyGenerator_test_2.stdout 2> TOPP_OpenSwathDecoyGenerator_test_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
504 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathDecoyGenerator_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathDecoyGenerator_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathDecoyGenerator_test_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
505 OpenSwathDecoyGenerator -test -in OpenSwathDecoyGenerator_input_3.TraML -out OpenSwathDecoyGenerator_3.TraML.tmp -out_type TraML -method pseudo-reverse -separate -switchKR false > TOPP_OpenSwathDecoyGenerator_test_3.stdout 2> TOPP_OpenSwathDecoyGenerator_test_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
506 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathDecoyGenerator_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathDecoyGenerator_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathDecoyGenerator_test_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
507 OpenSwathDecoyGenerator -test -in OpenSwathDecoyGenerator_input_4.tsv -out OpenSwathDecoyGenerator_4.TraML.tmp -out_type TraML -method pseudo-reverse -separate -switchKR true -enable_detection_unspecific_losses -enable_detection_specific_losses -min_decoy_fraction 0.4 > TOPP_OpenSwathDecoyGenerator_test_4.stdout 2> TOPP_OpenSwathDecoyGenerator_test_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
508 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathDecoyGenerator_test_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathDecoyGenerator_test_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathDecoyGenerator_test_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
509 TargetedFileConverter -test -in ConvertTSVToTraML_1_input.tsv -out ConvertTSVToTraML_output.TraML.tmp -out_type TraML > TOPP_ConvertTSVToTraML_test_1.stdout 2> TOPP_ConvertTSVToTraML_test_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
510 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConvertTSVToTraML_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConvertTSVToTraML_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConvertTSVToTraML_test_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
511 TargetedFileConverter -test -in ConvertTSVToTraML_2_input.tsv -out ConvertTSVToTraML_2_output.TraML.tmp -algorithm:retentionTimeInterpretation minutes -out_type TraML > TOPP_ConvertTSVToTraML_test_2.stdout 2> TOPP_ConvertTSVToTraML_test_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
512 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConvertTSVToTraML_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConvertTSVToTraML_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConvertTSVToTraML_test_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
513 TargetedFileConverter -test -in ConvertTSVToTraML_2_input.tsv -out ConvertTSVToTraML_3_output.TraML.tmp -algorithm:retentionTimeInterpretation seconds -out_type TraML > TOPP_ConvertTSVToTraML_test_3.stdout 2> TOPP_ConvertTSVToTraML_test_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
514 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConvertTSVToTraML_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConvertTSVToTraML_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConvertTSVToTraML_test_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
515 TargetedFileConverter -test -in ConvertTSVToTraML_4_input.mrm -out ConvertTSVToTraML_4_output.TraML.tmp -out_type TraML > TOPP_ConvertTSVToTraML_test_4.stdout 2> TOPP_ConvertTSVToTraML_test_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
516 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConvertTSVToTraML_test_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConvertTSVToTraML_test_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConvertTSVToTraML_test_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
517 TargetedFileConverter -test -in ConvertTSVToTraML_5_input.tsv -out ConvertTSVToTraML_5_output.TraML.tmp -out_type TraML > TOPP_ConvertTSVToTraML_test_5.stdout 2> TOPP_ConvertTSVToTraML_test_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
518 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConvertTSVToTraML_test_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConvertTSVToTraML_test_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConvertTSVToTraML_test_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
519 TargetedFileConverter -test -in ConvertTSVToTraML_6_input.tsv -out ConvertTSVToTraML_6_output.TraML.tmp -out_type TraML > TOPP_ConvertTSVToTraML_test_6.stdout 2> TOPP_ConvertTSVToTraML_test_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
520 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConvertTSVToTraML_test_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConvertTSVToTraML_test_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConvertTSVToTraML_test_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
521 TargetedFileConverter -test -in ConvertTSVToTraML_7_input_Skyline.tsv -out ConvertTSVToTraML_7_output.TraML.tmp -out_type TraML > TOPP_ConvertTSVToTraML_test_7.stdout 2> TOPP_ConvertTSVToTraML_test_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
522 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConvertTSVToTraML_test_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConvertTSVToTraML_test_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConvertTSVToTraML_test_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
523 TargetedFileConverter -test -in TargetedFileConverter_1_input.TraML -out TargetedFileConverter_1_output.pqp.tmp -out_type pqp > TOPP_TargetedFileConverter_test_1_prepare.stdout 2> TOPP_TargetedFileConverter_test_1_prepare.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
524 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_1_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_1_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_1_prepare.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
525 TargetedFileConverter -test -in TargetedFileConverter_1_output.pqp.tmp -in_type pqp -out TargetedFileConverter_1_output.TraML.tmp -out_type TraML > TOPP_TargetedFileConverter_test_1.stdout 2> TOPP_TargetedFileConverter_test_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
526 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
527 TargetedFileConverter -test -in TargetedFileConverter_1_output.pqp.tmp -in_type pqp -out TargetedFileConverter_2_output.TraML.tmp -out_type TraML -legacy_traml_id > TOPP_TargetedFileConverter_test_2.stdout 2> TOPP_TargetedFileConverter_test_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
528 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
529 TargetedFileConverter -test -in TargetedFileConverter_3_input.TraML -out TargetedFileConverter_3_output.pqp.tmp -out_type pqp > TOPP_TargetedFileConverter_test_3_prepare.stdout 2> TOPP_TargetedFileConverter_test_3_prepare.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
530 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_3_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_3_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_3_prepare.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
531 TargetedFileConverter -test -in TargetedFileConverter_3_output.pqp.tmp -in_type pqp -out TargetedFileConverter_3_output.TraML.tmp -out_type TraML > TOPP_TargetedFileConverter_test_3.stdout 2> TOPP_TargetedFileConverter_test_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
532 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
533 TargetedFileConverter -test -in TargetedFileConverter_3_output.pqp.tmp -in_type pqp -out TargetedFileConverter_4_output.TraML.tmp -out_type TraML -legacy_traml_id > TOPP_TargetedFileConverter_test_4.stdout 2> TOPP_TargetedFileConverter_test_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
534 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
535 TargetedFileConverter -test -in TargetedFileConverter_10_input.pqp -out TargetedFileConverter_10_output.TraML.tmp -out_type TraML -legacy_traml_id > TOPP_TargetedFileConverter_test_10_prepare.stdout 2> TOPP_TargetedFileConverter_test_10_prepare.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
536 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_10_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_10_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_10_prepare.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
537 TargetedFileConverter -test -in TargetedFileConverter_10_output.TraML.tmp -in_type TraML -out TargetedFileConverter_10_output.tsv.tmp -out_type tsv > TOPP_TargetedFileConverter_test_10.stdout 2> TOPP_TargetedFileConverter_test_10.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
538 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_10.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
539 TargetedFileConverter -test -in TargetedFileConverter_11_input.TraML -out TargetedFileConverter_11_output.pqp.tmp -out_type pqp > TOPP_TargetedFileConverter_test_11_prepare.stdout 2> TOPP_TargetedFileConverter_test_11_prepare.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
540 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_11_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_11_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_11_prepare.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
541 TargetedFileConverter -test -in TargetedFileConverter_11_output.pqp.tmp -in_type pqp -out TargetedFileConverter_11_output.TraML.tmp -out_type TraML > TOPP_TargetedFileConverter_test_11.stdout 2> TOPP_TargetedFileConverter_test_11.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
542 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_11.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
543 TargetedFileConverter -algorithm:override_group_label_check -test -in TargetedFileConverter_8_input.tsv -out TargetedFileConverter_8_output.TraML.tmp -out_type TraML > TOPP_TargetedFileConverter_test_8_prepare.stdout 2> TOPP_TargetedFileConverter_test_8_prepare.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
544 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_8_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_8_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_8_prepare.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
545 TargetedFileConverter -algorithm:override_group_label_check -test -in TargetedFileConverter_8_output.TraML.tmp -in_type TraML -out TargetedFileConverter_8_output.tsv.tmp -out_type tsv > TOPP_TargetedFileConverter_test_8.stdout 2> TOPP_TargetedFileConverter_test_8.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
546 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_8.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
547 TargetedFileConverter -algorithm:override_group_label_check -test -in TargetedFileConverter_9_input.TraML -out TargetedFileConverter_9_output.pqp.tmp -out_type pqp > TOPP_TargetedFileConverter_test_9_prepare.stdout 2> TOPP_TargetedFileConverter_test_9_prepare.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
548 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_9_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_9_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_9_prepare.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
549 TargetedFileConverter -algorithm:override_group_label_check -test -in TargetedFileConverter_9_output.pqp.tmp -in_type pqp -out TargetedFileConverter_9_output.TraML.tmp -out_type TraML > TOPP_TargetedFileConverter_test_9.stdout 2> TOPP_TargetedFileConverter_test_9.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
550 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_9.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
551 TargetedFileConverter -test -in ConvertTSVToTraML_output.TraML -out ConvertTraMLToTSV_output.tmp.tsv -out_type tsv > TOPP_TargetedFileConverter_test_5.stdout 2> TOPP_TargetedFileConverter_test_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
552 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
553 TargetedFileConverter -algorithm:override_group_label_check -test -in TargetedFileConverter_12_input.TraML -out TargetedFileConverter_12_output.pqp.tmp -out_type pqp > TOPP_TargetedFileConverter_test_12_prepare.stdout 2> TOPP_TargetedFileConverter_test_12_prepare.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
554 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_12_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_12_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_12_prepare.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
555 TargetedFileConverter -algorithm:override_group_label_check -test -in TargetedFileConverter_12_output.pqp.tmp -in_type pqp -out TargetedFileConverter_12_output.TraML.tmp -out_type TraML > TOPP_TargetedFileConverter_test_12.stdout 2> TOPP_TargetedFileConverter_test_12.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
556 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_12.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
557 TargetedFileConverter -test -in TargetedFileConverter_12_input.tsv -out TargetedFileConverter_13_output.TraML.tmp -out_type TraML > TOPP_TargetedFileConverter_test_13.stdout 2> TOPP_TargetedFileConverter_test_13.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
558 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_13.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
559 TargetedFileConverter -test -in ConvertTSVToTraML_5_output.TraML -out ConvertTraMLToTSV_output_2.tmp.tsv -out_type tsv > TOPP_TargetedFileConverter_test_6.stdout 2> TOPP_TargetedFileConverter_test_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
560 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
561 TargetedFileConverter -test -in ConvertTraMLToTSV_output_2.tmp.tsv -in_type tsv -out ConvertTraMLToTSV_output_2.tsv.back.tmp -out_type TraML > TOPP_TargetedFileConverter_test_6_convert_back.stdout 2> TOPP_TargetedFileConverter_test_6_convert_back.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
562 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_6_convert_back failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_6_convert_back.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_6_convert_back.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
563 MRMMapper -in MRMMapping_input.chrom.mzML -tr MRMMapping_input.TraML -out MRMMapping_output_1.chrom.mzML.tmp -test -algorithm:precursor_tolerance 0.3 -algorithm:product_tolerance 0.3 > TOPP_MRMMapper_test_1.stdout 2> TOPP_MRMMapper_test_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
564 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MRMMapper_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MRMMapper_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MRMMapper_test_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
565 MRMMapper -in MRMMapping_input.chrom.mzML -tr MRMMapping_input_2.TraML -out MRMMapping_output_2.chrom.mzML.tmp -test -algorithm:precursor_tolerance 0.01 -algorithm:product_tolerance 0.01 > TOPP_MRMMapper_test_2.stdout 2> TOPP_MRMMapper_test_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
566 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MRMMapper_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MRMMapper_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MRMMapper_test_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
567 OpenSwathFeatureXMLToTSV -in OpenSwathFeatureXMLToTSV_input.featureXML -tr OpenSwathFeatureXMLToTSV_input.TraML -out OpenSwathFeatureXMLToTSV_output.short.csv.tmp -short_format -test > TOPP_OpenSwathFeatureXMLToTSV_test_1.stdout 2> TOPP_OpenSwathFeatureXMLToTSV_test_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
568 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathFeatureXMLToTSV_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathFeatureXMLToTSV_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathFeatureXMLToTSV_test_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
569 OpenSwathFeatureXMLToTSV -in OpenSwathFeatureXMLToTSV_input.featureXML -tr OpenSwathFeatureXMLToTSV_input.TraML -out OpenSwathFeatureXMLToTSV_output.long.csv.tmp -test > TOPP_OpenSwathFeatureXMLToTSV_test_2.stdout 2> TOPP_OpenSwathFeatureXMLToTSV_test_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
570 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathFeatureXMLToTSV_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathFeatureXMLToTSV_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathFeatureXMLToTSV_test_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
571 OpenSwathFeatureXMLToTSV -in OpenSwathFeatureXMLToTSV_input.featureXML -tr OpenSwathFeatureXMLToTSV_input.TraML -out OpenSwathFeatureXMLToTSV_3_output.short.csv.tmp -short_format -best_scoring_peptide main_var_xx_lda_prelim_score -test > TOPP_OpenSwathFeatureXMLToTSV_test_3.stdout 2> TOPP_OpenSwathFeatureXMLToTSV_test_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
572 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathFeatureXMLToTSV_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathFeatureXMLToTSV_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathFeatureXMLToTSV_test_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
573 OpenSwathChromatogramExtractor -in OpenSwathChromatogramExtractor_input.mzML -tr OpenSwathChromatogramExtractor_input.TraML -out OpenSwathChromatogramExtractor_output.mzML.tmp -test > TOPP_OpenSwathChromatogramExtractor_test_1.stdout 2> TOPP_OpenSwathChromatogramExtractor_test_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
574 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathChromatogramExtractor_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
575 OpenSwathChromatogramExtractor -in OpenSwathChromatogramExtractor_input.mzML -tr OpenSwathChromatogramExtractor_input.TraML -rt_norm OpenSwathChromatogramExtractor_input.trafoXML -out OpenSwathChromatogramExtractor_output_2.mzML.tmp -test -rt_window 50 > TOPP_OpenSwathChromatogramExtractor_test_2.stdout 2> TOPP_OpenSwathChromatogramExtractor_test_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
576 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathChromatogramExtractor_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
577 OpenSwathChromatogramExtractor -in OpenSwathChromatogramExtractor_input.mzML -tr OpenSwathChromatogramExtractor_input.TraML -out OpenSwathChromatogramExtractor_output_3.mzML.tmp -test -extract_MS1 > TOPP_OpenSwathChromatogramExtractor_test_3.stdout 2> TOPP_OpenSwathChromatogramExtractor_test_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
578 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathChromatogramExtractor_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
579 OpenSwathChromatogramExtractor -in OpenSwathChromatogramExtractor_4_input.mzML -tr OpenSwathChromatogramExtractor_4_input.TraML -out OpenSwathChromatogramExtractor_output_4.mzML.tmp -ion_mobility_window 0.05 -is_swath -test > TOPP_OpenSwathChromatogramExtractor_test_4.stdout 2> TOPP_OpenSwathChromatogramExtractor_test_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
580 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathChromatogramExtractor_test_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
581 OpenSwathChromatogramExtractor -in OpenSwathChromatogramExtractor_input.mzML -tr OpenSwathChromatogramExtractor_5_input.TraML -out OpenSwathChromatogramExtractor_5_output.mzML.tmp -test -extract_MS1 > TOPP_OpenSwathChromatogramExtractor_test_5.stdout 2> TOPP_OpenSwathChromatogramExtractor_test_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
582 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathChromatogramExtractor_test_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
583 OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_1_output.featureXML.tmp -rt_norm OpenSwathAnalyzer_input.trafoXML -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -test > TOPP_OpenSwathAnalyzer_test_1.stdout 2> TOPP_OpenSwathAnalyzer_test_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
584 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
585 OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_2_output.featureXML.tmp -swath_files OpenSwathAnalyzer_2_swathfile.mzML -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -test > TOPP_OpenSwathAnalyzer_test_2.stdout 2> TOPP_OpenSwathAnalyzer_test_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
586 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
587 OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_mod_input.TraML -out OpenSwathAnalyzer_5_output.featureXML.tmp -swath_files OpenSwathAnalyzer_2_swathfile.mzML -ini OpenSwathAnalyzer_5.ini -test > TOPP_OpenSwathAnalyzer_test_5_mod.stdout 2> TOPP_OpenSwathAnalyzer_test_5_mod.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
588 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_5_mod failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_5_mod.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_5_mod.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
589 OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_6_output.featureXML.tmp -swath_files OpenSwathAnalyzer_2_swathfile.mzML -ini OpenSwathAnalyzer_5.ini -test > TOPP_OpenSwathAnalyzer_test_6_nomod.stdout 2> TOPP_OpenSwathAnalyzer_test_6_nomod.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
590 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_6_nomod failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_6_nomod.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_6_nomod.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
591 OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_7_output.featureXML.tmp -ini OpenSwathAnalyzer_7_backgroundSubtraction.ini -test > TOPP_OpenSwathAnalyzer_test_7_backgroundSubtraction.stdout 2> TOPP_OpenSwathAnalyzer_test_7_backgroundSubtraction.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
592 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_7_backgroundSubtraction failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_7_backgroundSubtraction.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_7_backgroundSubtraction.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
593 OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_8_output.featureXML.tmp -rt_norm OpenSwathAnalyzer_input.trafoXML -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -algorithm:Scores:use_ms1_mi -algorithm:Scores:use_mi_score -algorithm:Scores:use_total_mi_score -test > TOPP_OpenSwathAnalyzer_test_8.stdout 2> TOPP_OpenSwathAnalyzer_test_8.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
594 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_8.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
595 OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_9_output.featureXML.tmp -rt_norm OpenSwathAnalyzer_input.trafoXML -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -algorithm:Scores:use_mi_score -test > TOPP_OpenSwathAnalyzer_test_9.stdout 2> TOPP_OpenSwathAnalyzer_test_9.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
596 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_9.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
597 OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_10_output.featureXML.tmp -rt_norm OpenSwathAnalyzer_input.trafoXML -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -algorithm:Scores:use_mi_score -algorithm:Scores:use_total_mi_score -test > TOPP_OpenSwathAnalyzer_test_10.stdout 2> TOPP_OpenSwathAnalyzer_test_10.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
598 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_10.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
599 OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_11_output.featureXML.tmp -rt_norm OpenSwathAnalyzer_input.trafoXML -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -algorithm:Scores:use_total_mi_score -test > TOPP_OpenSwathAnalyzer_test_11.stdout 2> TOPP_OpenSwathAnalyzer_test_11.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
600 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_11.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
601 OpenSwathRTNormalizer -in OpenSwathRTNormalizer_1_input.mzML -tr OpenSwathRTNormalizer_1_input.TraML -out OpenSwathRTNormalizer_1_output.trafoXML.tmp -test > TOPP_OpenSwathRTNormalizer_test_1.stdout 2> TOPP_OpenSwathRTNormalizer_test_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
602 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathRTNormalizer_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathRTNormalizer_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathRTNormalizer_test_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
603 OpenSwathRTNormalizer -in OpenSwathRTNormalizer_1_input.mzML -tr OpenSwathRTNormalizer_1_input.TraML -out OpenSwathRTNormalizer_3_output.trafoXML.tmp -test -estimateBestPeptides -peptideEstimation:NrRTBins 3 -peptideEstimation:MinBinsFilled 3 > TOPP_OpenSwathRTNormalizer_test_3.stdout 2> TOPP_OpenSwathRTNormalizer_test_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
604 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathRTNormalizer_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathRTNormalizer_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathRTNormalizer_test_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
605 OpenSwathRTNormalizer -in OpenSwathRTNormalizer_1_input.mzML -tr OpenSwathRTNormalizer_1_input.TraML -out OpenSwathRTNormalizer_4_output.trafoXML.tmp -test -RTNormalization:outlierMethod iter_residual > TOPP_OpenSwathRTNormalizer_test_4.stdout 2> TOPP_OpenSwathRTNormalizer_test_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
606 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathRTNormalizer_test_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathRTNormalizer_test_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathRTNormalizer_test_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
607 OpenSwathConfidenceScoring -test -in OpenSwathFeatureXMLToTSV_input.featureXML -lib OpenSwathFeatureXMLToTSV_input.TraML -trafo OpenSwathConfidenceScoring_1_input.trafoXML -transitions 2 -decoys 1 -out OpenSwathConfidenceScoring_1_output.tmp > TOPP_OpenSwathConfidenceScoring_1.stdout 2> TOPP_OpenSwathConfidenceScoring_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
608 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathConfidenceScoring_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathConfidenceScoring_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathConfidenceScoring_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
609 OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_1_input.mzML -out OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML -test > TOPP_OpenSwathMzMLFileCacher_test_1_step1.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_1_step1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
610 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_1_step1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_1_step1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_1_step1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
611 OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML -out OpenSwathMzMLFileCacher_1_output.tmp.mzML -convert_back -test > TOPP_OpenSwathMzMLFileCacher_test_1_step2.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_1_step2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
612 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_1_step2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_1_step2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_1_step2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
613 OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_2_input.chrom.mzML -out OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML -test > TOPP_OpenSwathMzMLFileCacher_test_2_step1.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_2_step1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
614 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_2_step1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_2_step1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_2_step1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
615 OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML -out OpenSwathMzMLFileCacher_2_output.chrom.tmp.mzML -convert_back -test > TOPP_OpenSwathMzMLFileCacher_test_2_step2.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_2_step2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
616 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_2_step2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_2_step2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_2_step2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
617 OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_1_input.mzML -out OpenSwathMzMLFileCacher_3_input.tmp.sqMass -test -lossy_compression true -lossy_mass_accuracy 1e-4 > TOPP_OpenSwathMzMLFileCacher_test_3_step1.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_3_step1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
618 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_3_step1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_3_step1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_3_step1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
619 OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_3_input.tmp.sqMass -out OpenSwathMzMLFileCacher_3_output.tmp.mzML -test > TOPP_OpenSwathMzMLFileCacher_test_3_step2.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_3_step2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
620 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_3_step2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_3_step2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_3_step2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
621 OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_2_input.chrom.mzML -out OpenSwathMzMLFileCacher_4_input.tmp.sqMass -test > TOPP_OpenSwathMzMLFileCacher_test_4_step1.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_4_step1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
622 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_4_step1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_4_step1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_4_step1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
623 OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_4_input.tmp.sqMass -out OpenSwathMzMLFileCacher_4_output.tmp.mzML -test > TOPP_OpenSwathMzMLFileCacher_test_4_step2.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_4_step2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
624 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_4_step2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_4_step2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_4_step2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
625 OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_1_input.mzML -out OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML -test -process_lowmemory > TOPP_OpenSwathMzMLFileCacher_test_5_step1.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_5_step1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
626 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_5_step1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_5_step1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_5_step1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
627 OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML -out OpenSwathMzMLFileCacher_1_output.tmp.mzML -convert_back -test > TOPP_OpenSwathMzMLFileCacher_test_5_step2.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_5_step2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
628 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_5_step2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_5_step2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_5_step2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
629 OpenSwathMzMLFileCacher -in OpenSwathAnalyzer_2_swathfile.mzML -out OpenSwathAnalyzer_3_swathfile.mzML.cached.tmp -out_type mzML -test > TOPP_OpenSwathAnalyzer_test_3_prepare.stdout 2> TOPP_OpenSwathAnalyzer_test_3_prepare.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
630 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_3_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_3_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_3_prepare.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
631 OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out MRMFeatureFinderScore_output_3.featureXML.tmp -swath_files OpenSwathAnalyzer_3_swathfile.mzML.cached.tmp -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -test > TOPP_OpenSwathAnalyzer_test_3.stdout 2> TOPP_OpenSwathAnalyzer_test_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
632 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
633 OpenSwathMzMLFileCacher -in OpenSwathAnalyzer_2_swathfile.mzML -out OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp -out_type mzML -test > TOPP_OpenSwathAnalyzer_test_4_prepare1.stdout 2> TOPP_OpenSwathAnalyzer_test_4_prepare1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
634 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_4_prepare1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_4_prepare1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_4_prepare1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
635 OpenSwathMzMLFileCacher -in OpenSwathAnalyzer_1_input_chrom.mzML -out OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp -out_type mzML -test > TOPP_OpenSwathAnalyzer_test_4_prepare2.stdout 2> TOPP_OpenSwathAnalyzer_test_4_prepare2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
636 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_4_prepare2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_4_prepare2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_4_prepare2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
637 OpenSwathAnalyzer -in OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp -tr OpenSwathAnalyzer_1_input.TraML -out MRMFeatureFinderScore_output_4.featureXML.tmp -swath_files OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -test > TOPP_OpenSwathAnalyzer_test_4.stdout 2> TOPP_OpenSwathAnalyzer_test_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
638 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
639 MRMTransitionGroupPicker -in MRMTransitionGroupPicker_1_input.mzML -tr MRMTransitionGroupPicker_1_input.TraML -out MRMTransitionGroupPicker_test_1.featureXML.tmp -test -algorithm:PeakPickerMRM:remove_overlapping_peaks true -algorithm:PeakPickerMRM:method legacy -algorithm:PeakPickerMRM:peak_width 40.0 > UTILS_MRMTransitionGroupPicker_test_1.stdout 2> UTILS_MRMTransitionGroupPicker_test_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
640 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MRMTransitionGroupPicker_test_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MRMTransitionGroupPicker_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MRMTransitionGroupPicker_test_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
641 MRMTransitionGroupPicker -in MRMTransitionGroupPicker_1_input.mzML -tr MRMTransitionGroupPicker_1_input.TraML -out MRMTransitionGroupPicker_test_2.featureXML.tmp -test -algorithm:PeakPickerMRM:remove_overlapping_peaks true -algorithm:PeakPickerMRM:method legacy -algorithm:PeakPickerMRM:peak_width 40.0 -algorithm:compute_total_mi > UTILS_MRMTransitionGroupPicker_test_2.stdout 2> UTILS_MRMTransitionGroupPicker_test_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
642 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MRMTransitionGroupPicker_test_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MRMTransitionGroupPicker_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MRMTransitionGroupPicker_test_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
643 OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_1.chrom.mzML.tmp -out_features OpenSwathWorkflow_1.featureXML.tmp -out_qc OpenSwathWorkflow_1.json.tmp -test > TOPP_OpenSwathWorkflow_1.stdout 2> TOPP_OpenSwathWorkflow_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
644 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
645 OpenSwathWorkflow -in OpenSwathWorkflow_2_input.mzXML -tr OpenSwathWorkflow_2_input.TraML -rt_norm OpenSwathWorkflow_2_input.trafoXML -out_chrom OpenSwathWorkflow_2.chrom.mzML.tmp -out_features OpenSwathWorkflow_2.featureXML.tmp -test > TOPP_OpenSwathWorkflow_2.stdout 2> TOPP_OpenSwathWorkflow_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
646 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
647 OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_3.chrom.mzML.tmp -out_features OpenSwathWorkflow_3.featureXML.tmp -test -use_ms1_traces > TOPP_OpenSwathWorkflow_3.stdout 2> TOPP_OpenSwathWorkflow_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
648 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
649 OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_4.chrom.mzML.tmp -out_tsv OpenSwathWorkflow_4.tsv.tmp -test -use_ms1_traces > TOPP_OpenSwathWorkflow_4.stdout 2> TOPP_OpenSwathWorkflow_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
650 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
651 OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_5.chrom.mzML.tmp -out_features OpenSwathWorkflow_5.featureXML.tmp -test -use_ms1_traces -readOptions cache -tempDirectory "." > TOPP_OpenSwathWorkflow_5.stdout 2> TOPP_OpenSwathWorkflow_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
652 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
653 OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_6.chrom.mzML.tmp -out_features OpenSwathWorkflow_6.featureXML.tmp -test -use_ms1_traces -readOptions cacheWorkingInMemory -tempDirectory "." > TOPP_OpenSwathWorkflow_6.stdout 2> TOPP_OpenSwathWorkflow_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
654 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
655 OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_7.chrom.mzML.tmp -out_features OpenSwathWorkflow_7.featureXML.tmp -test -use_ms1_traces -swath_windows_file swath_windows.txt > TOPP_OpenSwathWorkflow_7.stdout 2> TOPP_OpenSwathWorkflow_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
656 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
657 OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_10.chrom.mzML.tmp -out_features OpenSwathWorkflow_10.featureXML.tmp -test -use_ms1_traces -swath_windows_file swath_windows_overlap.txt -force > TOPP_OpenSwathWorkflow_10.stdout 2> TOPP_OpenSwathWorkflow_10.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
658 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_10.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
659 OpenSwathWorkflow -in OpenSwathWorkflow_11_input.mzML -tr_irt OpenSwathWorkflow_11_input.TraML -tr OpenSwathWorkflow_11_input.TraML -mz_extraction_window 0.2 -rt_extraction_window -1 -Scoring:Scores:use_sonar_scores -sonar -out_chrom OpenSwathWorkflow_11.chrom.mzML.tmp -out_features OpenSwathWorkflow_11.featureXML.tmp -RTNormalization:outlierMethod none -mz_correction_function quadratic_regression_delta_ppm -irt_mz_extraction_window 550 -irt_mz_extraction_window_unit ppm -test > TOPP_OpenSwathWorkflow_11.stdout 2> TOPP_OpenSwathWorkflow_11.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
660 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_11.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
661 TargetedFileConverter -test -in OpenSwathWorkflow_1_input.TraML -out OpenSwathWorkflow_13_input.pqp.tmp -out_type pqp > TOPP_OpenSwathWorkflow_13_prepare.stdout 2> TOPP_OpenSwathWorkflow_13_prepare.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
662 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_13_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_13_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_13_prepare.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
663 OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_13_input.pqp.tmp -tr_type pqp -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_13.chrom.mzML.tmp -out_osw OpenSwathWorkflow_13.osw -test -use_ms1_traces > TOPP_OpenSwathWorkflow_13.stdout 2> TOPP_OpenSwathWorkflow_13.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
664 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_13.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
665 TargetedFileConverter -test -in OpenSwathWorkflow_1_input.TraML -out OpenSwathWorkflow_14_input.pqp.tmp -out_type pqp > TOPP_OpenSwathWorkflow_14_prepare.stdout 2> TOPP_OpenSwathWorkflow_14_prepare.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
666 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_14_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_14_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_14_prepare.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
667 OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_14_input.pqp.tmp -tr_type pqp -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_14.chrom.tmp.sqMass -out_osw OpenSwathWorkflow_14.osw -test -use_ms1_traces > TOPP_OpenSwathWorkflow_14.stdout 2> TOPP_OpenSwathWorkflow_14.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
668 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_14.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
669 OpenSwathMzMLFileCacher -in OpenSwathWorkflow_14.chrom.tmp.sqMass -out OpenSwathWorkflow_14.chrom.tmp.mzML -test -lossy_compression false -lossy_mass_accuracy 1e-4 -full_meta false > TOPP_OpenSwathWorkflow_14_step2.stdout 2> TOPP_OpenSwathWorkflow_14_step2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
670 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_14_step2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_14_step2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_14_step2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
671 OpenSwathWorkflow -in OpenSwathWorkflow_15_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_15.chrom.mzML.tmp -out_features OpenSwathWorkflow_15.featureXML.tmp -test -use_ms1_traces -Scoring:TransitionGroupPicker:compute_peak_quality false -Scoring:TransitionGroupPicker:use_precursors -ms1_isotopes 2 > TOPP_OpenSwathWorkflow_15.stdout 2> TOPP_OpenSwathWorkflow_15.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
672 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_15 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_15.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_15.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
673 OpenSwathMzMLFileCacher -in OpenSwathWorkflow_1_input.mzML -out OpenSwathWorkflow_16_input.sqMass -test -lossy_compression true -lossy_mass_accuracy 1e-4 -full_meta true > TOPP_OpenSwathWorkflow_16_prepare.stdout 2> TOPP_OpenSwathWorkflow_16_prepare.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
674 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_16_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_16_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_16_prepare.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
675 OpenSwathWorkflow -in OpenSwathWorkflow_16_input.sqMass -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_16.chrom.mzML.tmp -out_features OpenSwathWorkflow_16.featureXML.tmp -test -use_ms1_traces -readOptions workingInMemory -ms1_isotopes 2 > TOPP_OpenSwathWorkflow_16.stdout 2> TOPP_OpenSwathWorkflow_16.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
676 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_16 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_16.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_16.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
677 OpenSwathWorkflow -in OpenSwathWorkflow_17_input.mzML -tr OpenSwathWorkflow_17_input.tsv -out_chrom OpenSwathWorkflow_17.chrom.mzML.tmp -out_features OpenSwathWorkflow_17.featureXML.tmp -test -use_ms1_traces -readOptions workingInMemory -ion_mobility_window 0.05 -use_ms1_ion_mobility "false" -Scoring:Scores:use_ion_mobility_scores > TOPP_OpenSwathWorkflow_17.stdout 2> TOPP_OpenSwathWorkflow_17.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
678 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_17 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_17.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_17.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
679 OpenSwathWorkflow -in OpenSwathWorkflow_17_input.mzML -tr OpenSwathWorkflow_17_input.tsv -out_chrom OpenSwathWorkflow_17.chrom.mzML.tmp -out_features OpenSwathWorkflow_17.featureXML.tmp -test -use_ms1_traces -readOptions cache -ion_mobility_window 0.05 -use_ms1_ion_mobility "false" -Scoring:Scores:use_ion_mobility_scores > TOPP_OpenSwathWorkflow_17_cache.stdout 2> TOPP_OpenSwathWorkflow_17_cache.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
680 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_17_cache failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_17_cache.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_17_cache.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
681 TargetedFileConverter -test -in OpenSwathWorkflow_17_input.tsv -out OpenSwathWorkflow_17_input.pqp.tmp -out_type pqp > TOPP_OpenSwathWorkflow_17_b_prepare.stdout 2> TOPP_OpenSwathWorkflow_17_b_prepare.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
682 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_17_b_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_17_b_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_17_b_prepare.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
683 OpenSwathWorkflow -in OpenSwathWorkflow_17_input.mzML -tr_type pqp -tr OpenSwathWorkflow_17_input.pqp.tmp -out_chrom OpenSwathWorkflow_17_b.chrom.mzML.tmp -out_features OpenSwathWorkflow_17_b.featureXML.tmp -test -use_ms1_traces -readOptions workingInMemory -ion_mobility_window 0.05 -use_ms1_ion_mobility "false" > TOPP_OpenSwathWorkflow_17_b.stdout 2> TOPP_OpenSwathWorkflow_17_b.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
684 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_17_b failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_17_b.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_17_b.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
685 OpenSwathFileSplitter -in OpenSwathWorkflow_1_input.mzML -outputDirectory "" -out_qc OpenSwathFileSplitter_1.json.tmp -test > TOPP_OpenSwathFileSplitter_1.stdout 2> TOPP_OpenSwathFileSplitter_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
686 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathFileSplitter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathFileSplitter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathFileSplitter_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
687 OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_features OpenSwathWorkflow_18.featureXML.tmp -test -use_ms1_traces -Scoring:Scores:use_ms1_mi > TOPP_OpenSwathWorkflow_18.stdout 2> TOPP_OpenSwathWorkflow_18.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
688 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_18 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_18.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_18.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
689 OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_features OpenSwathWorkflow_19.featureXML.tmp -test -use_ms1_traces -Scoring:Scores:use_mi_score > TOPP_OpenSwathWorkflow_19.stdout 2> TOPP_OpenSwathWorkflow_19.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
690 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_19 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_19.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_19.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
691 OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_features OpenSwathWorkflow_20.featureXML.tmp -test -use_ms1_traces -Scoring:Scores:use_mi_score -Scoring:Scores:use_total_mi_score > TOPP_OpenSwathWorkflow_20.stdout 2> TOPP_OpenSwathWorkflow_20.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
692 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_20 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_20.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_20.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
693 OpenSwathWorkflow -in OpenSwathWorkflow_21_input.mzML -tr OpenSwathWorkflow_21_input.tsv -tr_irt OpenSwathWorkflow_21_input.irt.TraML -out_features OpenSwathWorkflow_21.featureXML.tmp -Debugging:irt_trafo OpenSwathWorkflow_21.trafoXML.tmp -out_chrom OpenSwathWorkflow_21.mzML.tmp -test -use_ms1_traces -Scoring:Scores:use_mi_score -Scoring:Scores:use_total_mi_score > TOPP_OpenSwathWorkflow_21.stdout 2> TOPP_OpenSwathWorkflow_21.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
694 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_21 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_21.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_21.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
695 OpenSwathWorkflow -in OpenSwathWorkflow_22_input.mzML -tr OpenSwathWorkflow_22_input.tsv -out_chrom OpenSwathWorkflow_22.chrom.mzML.tmp -out_features OpenSwathWorkflow_22.featureXML.tmp -test -use_ms1_traces -readOptions workingInMemory -matching_window_only "true" -ms1_isotopes 3 > TOPP_OpenSwathWorkflow_22.stdout 2> TOPP_OpenSwathWorkflow_22.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
696 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_22 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_22.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_22.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
697 NoiseFilterGaussian -test -ini NoiseFilterGaussian_1_parameters.ini -in NoiseFilterGaussian_1_input.mzML -out NoiseFilterGaussian_1.tmp > TOPP_NoiseFilterGaussian_1.stdout 2> TOPP_NoiseFilterGaussian_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
698 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterGaussian_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterGaussian_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterGaussian_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
699 NoiseFilterGaussian -test -ini NoiseFilterGaussian_2_parameters.ini -in NoiseFilterGaussian_2_input.chrom.mzML -out NoiseFilterGaussian_2.tmp > TOPP_NoiseFilterGaussian_2.stdout 2> TOPP_NoiseFilterGaussian_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
700 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterGaussian_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterGaussian_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterGaussian_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
701 NoiseFilterGaussian -test -ini NoiseFilterGaussian_1_parameters.ini -in NoiseFilterGaussian_1_input.mzML -out NoiseFilterGaussian_3.tmp -processOption lowmemory > TOPP_NoiseFilterGaussian_3.stdout 2> TOPP_NoiseFilterGaussian_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
702 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterGaussian_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterGaussian_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterGaussian_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
703 NoiseFilterGaussian -test -ini NoiseFilterGaussian_2_parameters.ini -in NoiseFilterGaussian_2_input.chrom.mzML -out NoiseFilterGaussian_4.tmp -processOption lowmemory > TOPP_NoiseFilterGaussian_4.stdout 2> TOPP_NoiseFilterGaussian_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
704 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterGaussian_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterGaussian_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterGaussian_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
705 NoiseFilterSGolay -test -ini NoiseFilterSGolay_1_parameters.ini -in NoiseFilterSGolay_1_input.mzML -out NoiseFilterSGolay_1.tmp > TOPP_NoiseFilterSGolay_1.stdout 2> TOPP_NoiseFilterSGolay_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
706 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterSGolay_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterSGolay_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterSGolay_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
707 NoiseFilterSGolay -test -ini NoiseFilterSGolay_2_parameters.ini -in NoiseFilterSGolay_2_input.chrom.mzML -out NoiseFilterSGolay_2.tmp > TOPP_NoiseFilterSGolay_2.stdout 2> TOPP_NoiseFilterSGolay_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
708 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterSGolay_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterSGolay_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterSGolay_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
709 NoiseFilterSGolay -test -ini NoiseFilterSGolay_1_parameters.ini -in NoiseFilterSGolay_1_input.mzML -out NoiseFilterSGolay_3.tmp -processOption lowmemory > TOPP_NoiseFilterSGolay_3.stdout 2> TOPP_NoiseFilterSGolay_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
710 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterSGolay_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterSGolay_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterSGolay_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
711 NoiseFilterSGolay -test -ini NoiseFilterSGolay_2_parameters.ini -in NoiseFilterSGolay_2_input.chrom.mzML -out NoiseFilterSGolay_4.tmp -processOption lowmemory > TOPP_NoiseFilterSGolay_4.stdout 2> TOPP_NoiseFilterSGolay_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
712 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterSGolay_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterSGolay_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterSGolay_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
713 PeakPickerWavelet -test -ini PeakPickerWavelet_parameters.ini -in PeakPickerWavelet_input.mzML -out PeakPickerWavelet_1.tmp > TOPP_PeakPickerWavelet_1.stdout 2> TOPP_PeakPickerWavelet_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
714 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerWavelet_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerWavelet_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerWavelet_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
715 PeakPickerWavelet -test -ini PeakPickerWavelet_deconv_parameters.ini -in PeakPickerWavelet_deconv_input.mzML -out PeakPickerWavelet_2.tmp > TOPP_PeakPickerWavelet_2.stdout 2> TOPP_PeakPickerWavelet_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
716 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerWavelet_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerWavelet_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerWavelet_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
717 PeakPickerWavelet -test -ini PeakPickerWavelet_parameters.ini -in PeakPickerWavelet_input.mzML -out PeakPickerWavelet_4.tmp -threads 2 > TOPP_PeakPickerWavelet_4.stdout 2> TOPP_PeakPickerWavelet_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
718 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerWavelet_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerWavelet_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerWavelet_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
719 PeakPickerWavelet -test -ini PeakPickerWavelet_parameters_noMetaData.ini -in PeakPickerWavelet_input.mzML -out PeakPickerWavelet_5.tmp -threads 2 > TOPP_PeakPickerWavelet_5.stdout 2> TOPP_PeakPickerWavelet_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
720 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerWavelet_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerWavelet_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerWavelet_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
721 PeakPickerHiRes -test -ini PeakPickerHiRes_parameters.ini -in PeakPickerHiRes_input.mzML -out PeakPickerHiRes_1.tmp > TOPP_PeakPickerHiRes_1.stdout 2> TOPP_PeakPickerHiRes_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
722 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerHiRes_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerHiRes_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerHiRes_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
723 PeakPickerHiRes -test -ini PeakPickerHiRes_parameters.ini -in PeakPickerHiRes_2_input.mzML -out PeakPickerHiRes_2.tmp > TOPP_PeakPickerHiRes_2.stdout 2> TOPP_PeakPickerHiRes_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
724 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerHiRes_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerHiRes_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerHiRes_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
725 PeakPickerHiRes -test -ini PeakPickerHiRes_parameters.ini -in PeakPickerHiRes_input.mzML -out PeakPickerHiRes_3.tmp -processOption lowmemory > TOPP_PeakPickerHiRes_3.stdout 2> TOPP_PeakPickerHiRes_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
726 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerHiRes_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerHiRes_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerHiRes_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
727 PeakPickerHiRes -test -ini PeakPickerHiRes_parameters.ini -in PeakPickerHiRes_2_input.mzML -out PeakPickerHiRes_4.tmp -processOption lowmemory > TOPP_PeakPickerHiRes_4.stdout 2> TOPP_PeakPickerHiRes_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
728 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerHiRes_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerHiRes_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerHiRes_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
729 PeakPickerHiRes -test -in PeakPickerHiRes_5_input.mzML -out PeakPickerHiRes_5.tmp > TOPP_PeakPickerHiRes_5.stdout 2> TOPP_PeakPickerHiRes_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
730 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerHiRes_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerHiRes_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerHiRes_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
731 PeakPickerIterative -in PeakPickerIterative_1_input.mzML -ini PeakPickerIterative_1.ini -out PeakPickerIterative.mzML.tmp -test > UTILS_PeakPickerIterative_1.stdout 2> UTILS_PeakPickerIterative_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
732 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_PeakPickerIterative_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_PeakPickerIterative_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_PeakPickerIterative_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
733 PeakPickerIterative -in PeakPickerIterative_2_input.mzML -ini PeakPickerIterative_2.ini -out PeakPickerIterative_2.mzML.tmp -test > UTILS_PeakPickerIterative_2.stdout 2> UTILS_PeakPickerIterative_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
734 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_PeakPickerIterative_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_PeakPickerIterative_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_PeakPickerIterative_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
735 LowMemPeakPickerHiRes -test -ini LowMemPeakPickerHiRes_parameters.ini -in PeakPickerHiRes_input.mzML -out LowMemPeakPickerHiRes_1.tmp > TOPP_LowMemPeakPickerHiRes_1.stdout 2> TOPP_LowMemPeakPickerHiRes_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
736 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_LowMemPeakPickerHiRes_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_LowMemPeakPickerHiRes_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_LowMemPeakPickerHiRes_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
737 LowMemPeakPickerHiResRandomAccess -test -ini LowMemPeakPickerHiRes_RandomAccess_parameters.ini -in PeakPickerHiRes_RandomAccess_input.mzML -out LowMemPeakPickerHiRes_RandomAccess_1.tmp > TOPP_LowMemPeakPickerHiResRandomAccess_1.stdout 2> TOPP_LowMemPeakPickerHiResRandomAccess_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
738 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_LowMemPeakPickerHiResRandomAccess_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_LowMemPeakPickerHiResRandomAccess_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_LowMemPeakPickerHiResRandomAccess_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
739 ProteinInference -test -in ProteinInference_1_input.idXML -out ProteinInference_1_output.tmp -Algorithm:use_shared_peptides false -merge_runs all -Merging:annotate_origin false > TOPP_ProteinInference_1.stdout 2> TOPP_ProteinInference_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
740 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinInference_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinInference_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinInference_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
741 Resampler -test -in Resampler_1_input.mzML -out Resampler.mzML -sampling_rate 0.3 > TOPP_Resampler_1.stdout 2> TOPP_Resampler_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
742 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_Resampler_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_Resampler_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_Resampler_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
743 RNPxlSearch -test -in RNPxlSearch_1_input.mzML -database RNPxlSearch_1_input.fasta -out RNPxlSearch_1_output.tmp -ini RNPxlSearch_1_parameters.ini > TOPP_RNPxlSearch_1.stdout 2> TOPP_RNPxlSearch_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
744 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RNPxlSearch_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RNPxlSearch_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RNPxlSearch_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
745 RNPxlSearch -test -in RNPxlSearch_1_input.mzML -database RNPxlSearch_1_input.fasta -out RNPxlSearch_2_output.tmp -RNPxl:decoys -ini RNPxlSearch_1_parameters.ini > TOPP_RNPxlSearch_2.stdout 2> TOPP_RNPxlSearch_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
746 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RNPxlSearch_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RNPxlSearch_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RNPxlSearch_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
747 RNPxlSearch -test -in RNPxlSearch_1_input.mzML -database RNPxlSearch_1_input.fasta -out RNPxlSearch_3_output.tmp -report:top_hits 3 -out_tsv RNPxlSearch_3_output2.tmp -precursor:mass_tolerance 10 -RNPxl:scoring fast > TOPP_RNPxlSearch_3.stdout 2> TOPP_RNPxlSearch_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
748 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RNPxlSearch_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RNPxlSearch_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RNPxlSearch_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
749 RNPxlSearch -test -in RNPxlSearch_1_input.mzML -RNPxl:decoys -database RNPxlSearch_1_input.fasta -out RNPxlSearch_4_output.tmp -report:top_hits 2 -out_tsv RNPxlSearch_4_output2.tmp -precursor:mass_tolerance 10 -RNPxl:scoring fast > TOPP_RNPxlSearch_4.stdout 2> TOPP_RNPxlSearch_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
750 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RNPxlSearch_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RNPxlSearch_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RNPxlSearch_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
751 RTModel -test -in RTModel_1_input.idXML -out RTModel_1_output.tmp -ini RTModel_1_parameters.ini > TOPP_RTModel_1.stdout 2> TOPP_RTModel_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
752 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTModel_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTModel_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTModel_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
753 RTModel -test -in_positive RTModel_2_input_positive.idXML -in_negative RTModel_2_input_negative.idXML -out RTModel_2_output.tmp -ini RTModel_2_parameters.ini > TOPP_RTModel_2.stdout 2> TOPP_RTModel_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
754 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTModel_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTModel_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTModel_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
755 RTModel -test -in RTModel_3_input.idXML -out RTModel_3_output.tmp -ini RTModel_3_parameters.ini > TOPP_RTModel_3.stdout 2> TOPP_RTModel_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
756 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTModel_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTModel_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTModel_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
757 RTModel -test -in RTModel_4_input.txt -out RTModel_4_output.tmp -ini RTModel_4_parameters.ini > TOPP_RTModel_4.stdout 2> TOPP_RTModel_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
758 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTModel_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTModel_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTModel_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
759 PTModel -test -in_positive PTModel_1_input_positive.idXML -in_negative PTModel_1_input_negative.idXML -out PTModel_1_output.tmp -ini PTModel_1_parameters.ini > TOPP_PTModel_1.stdout 2> TOPP_PTModel_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
760 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PTModel_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PTModel_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PTModel_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
761 PTPredict -test -in PTPredict_1_input.idXML -out PTPredict_1_output.tmp -svm_model PTPredict_1_input.model > TOPP_PTPredict_1.stdout 2> TOPP_PTPredict_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
762 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PTPredict_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PTPredict_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PTPredict_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
763 RTPredict -test -in_id RTPredict_1_input.idXML -out_id:file RTPredict_1_output.tmp -total_gradient_time 3000 -svm_model RTPredict_1_input.model > TOPP_RTPredict_1.stdout 2> TOPP_RTPredict_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
764 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTPredict_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTPredict_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTPredict_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
765 RTPredict -test -in_id RTPredict_2_input.idXML -out_id:positive RTPredict_2_output_positive.tmp -out_id:negative RTPredict_2_output_negative.tmp -svm_model RTPredict_2_input.model -in_oligo_params RTPredict_2_input.model_additional_parameters.paramXML -in_oligo_trainset RTPredict_2_input.model_samples > TOPP_RTPredict_2.stdout 2> TOPP_RTPredict_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
766 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTPredict_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTPredict_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTPredict_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
767 RTPredict -test -in_id RTPredict_3_input.idXML -out_id:file RTPredict_3_output.tmp -total_gradient_time 1 -svm_model RTPredict_3_input.model -in_oligo_params RTPredict_3_input.model_additional_parameters.paramXML -in_oligo_trainset RTPredict_3_input.model_samples > TOPP_RTPredict_3.stdout 2> TOPP_RTPredict_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
768 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTPredict_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTPredict_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTPredict_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
769 RTPredict -test -in_text RTPredict_4_input.txt -out_text:file RTPredict_4_output.tmp -total_gradient_time 1 -svm_model RTPredict_4_input.model -in_oligo_params RTPredict_4_input.model_additional_parameters.paramXML -in_oligo_trainset RTPredict_4_input.model_samples > TOPP_RTPredict_4.stdout 2> TOPP_RTPredict_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
770 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTPredict_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTPredict_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTPredict_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
771 RTPredict -test -in_id RTPredict_5_input.idXML -out_text:file RTPredict_5_output.tmp -total_gradient_time 1 -svm_model RTPredict_5_input.model -in_oligo_params RTPredict_5_input.model_additional_parameters.paramXML -in_oligo_trainset RTPredict_5_input.model_samples > TOPP_RTPredict_5.stdout 2> TOPP_RTPredict_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
772 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTPredict_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTPredict_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTPredict_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
773 InspectAdapter -test -ini InspectAdapter_1_parameters.ini -trie_dbs Inspect_FASTAFile_test2.trie -in Inspect.mzXML -dbs Inspect_FASTAFile_test.fasta -inspect_in -out InspectAdapter_2_output.tmp > TOPP_InspectAdapter_1.stdout 2> TOPP_InspectAdapter_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
774 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InspectAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InspectAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InspectAdapter_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
775 InspectAdapter -test -ini InspectAdapter_1_parameters.ini -trie_dbs Inspect_FASTAFile_test2.trie -in Inspect.mzData -dbs Inspect_FASTAFile_test.fasta -inspect_in -out InspectAdapter_3_output.tmp > TOPP_InspectAdapter_2.stdout 2> TOPP_InspectAdapter_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
776 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InspectAdapter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InspectAdapter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InspectAdapter_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
777 SeedListGenerator -test -in PepXMLFile_test.mzML -out SeedListGenerator_1_output.tmp > TOPP_SeedListGenerator_1.stdout 2> TOPP_SeedListGenerator_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
778 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SeedListGenerator_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SeedListGenerator_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SeedListGenerator_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
779 SeedListGenerator -test -in IDMapper_1_output.featureXML -out SeedListGenerator_2_output.tmp > TOPP_SeedListGenerator_2.stdout 2> TOPP_SeedListGenerator_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
780 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SeedListGenerator_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SeedListGenerator_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SeedListGenerator_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
781 SeedListGenerator -test -in ConsensusXMLFile_1.consensusXML -out SeedListGenerator_3_output1.tmp SeedListGenerator_3_output2.tmp > TOPP_SeedListGenerator_3.stdout 2> TOPP_SeedListGenerator_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
782 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SeedListGenerator_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SeedListGenerator_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SeedListGenerator_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
783 SpectraFilterSqrtMower -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterSqrtMower.tmp > TOPP_SpectraFilterSqrtMower_1.stdout 2> TOPP_SpectraFilterSqrtMower_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
784 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SpectraFilterSqrtMower_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SpectraFilterSqrtMower_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SpectraFilterSqrtMower_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
785 SpectraFilterWindowMower -test -in SpectraFilterWindowMower_1_input.mzML -out SpectraFilterWindowMower_1.tmp > TOPP_SpectraFilterWindowMower_1.stdout 2> TOPP_SpectraFilterWindowMower_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
786 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SpectraFilterWindowMower_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SpectraFilterWindowMower_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SpectraFilterWindowMower_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
787 SpectraFilterWindowMower -test -in SpectraFilterWindowMower_2_input.mzML -out SpectraFilterWindowMower_2.tmp -ini SpectraFilterWindowMower_2_parameters.ini > TOPP_SpectraFilterWindowMower_2.stdout 2> TOPP_SpectraFilterWindowMower_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
788 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SpectraFilterWindowMower_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SpectraFilterWindowMower_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SpectraFilterWindowMower_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
789 InternalCalibration -test -in InternalCalibration_1_BSA1.mzML -cal:id_in InternalCalibration_1_BSA1_OMSSA.idXML -out InternalCalibration_1_BSA1_out.mzML.tmp -cal:model_type linear -RANSAC:enabled -RANSAC:iter 500 -RANSAC:threshold 1 -RT_chunking -1 -quality_control:models InternalCalibration_1_models.csv.tmp -quality_control:residuals InternalCalibration_1_residuals.csv.tmp -ms_level 1 > TOPP_InternalCalibration_1.stdout 2> TOPP_InternalCalibration_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
790 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InternalCalibration_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InternalCalibration_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InternalCalibration_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
791 InternalCalibration -test -in InternalCalibration_2_lockmass.mzML.gz -cal:lock_in InternalCalibration_2_lock.csv -out InternalCalibration_2_lockmass.mzML.tmp -cal:lock_require_mono -cal:model_type linear -RT_chunking 60 -quality_control:models InternalCalibration_2_models.csv.tmp -quality_control:residuals InternalCalibration_2_residuals.csv.tmp > TOPP_InternalCalibration_2.stdout 2> TOPP_InternalCalibration_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
792 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InternalCalibration_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InternalCalibration_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InternalCalibration_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
793 FileConverter -test -in InternalCalibration_2_lockmass.mzML.tmp -no_progress -out InternalCalibration_2_out_lockmass.dta2d.tmp -out_type dta2d > TOPP_InternalCalibration_2_convert.stdout 2> TOPP_InternalCalibration_2_convert.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
794 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InternalCalibration_2_convert failed'; >&2 echo -e "stderr:\n$(cat TOPP_InternalCalibration_2_convert.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InternalCalibration_2_convert.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
795 ExternalCalibration -test -in ExternalCalibration_1_input.mzML -out ExternalCalibration_1_MS1_out.mzML.tmp -offset -5.5 -slope 0.0001 -ms_level 1 > TOPP_ExternalCalibration_1_MS1.stdout 2> TOPP_ExternalCalibration_1_MS1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
796 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ExternalCalibration_1_MS1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ExternalCalibration_1_MS1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ExternalCalibration_1_MS1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
797 ExternalCalibration -test -in ExternalCalibration_1_input.mzML -out ExternalCalibration_2_MS2_out.mzML.tmp -offset -5.5 -slope 0.0001 -ms_level 2 > TOPP_ExternalCalibration_2_MS2.stdout 2> TOPP_ExternalCalibration_2_MS2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
798 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ExternalCalibration_2_MS2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ExternalCalibration_2_MS2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ExternalCalibration_2_MS2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
799 TOFCalibration -test -in TOFCalibration_1_input.mzML -out TOFCalibration.tmp -ref_masses TOFCalibration_ref_masses.txt -ini TOFCalibration_parameters.ini -tof_const TOFCalibration_const.csv -ext_calibrants TOFCalibration_1_calibrants.mzML > TOPP_TOFCalibration_1.stdout 2> TOPP_TOFCalibration_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
800 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TOFCalibration_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TOFCalibration_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TOFCalibration_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
801 TOFCalibration -test -in TOFCalibration_2_input.mzML -out TOFCalibration_2.tmp -ref_masses TOFCalibration_ref_masses.txt -ini TOFCalibration_parameters.ini -tof_const TOFCalibration_const.csv -ext_calibrants TOFCalibration_2_calibrants.mzML -peak_data > TOPP_TOFCalibration_2.stdout 2> TOPP_TOFCalibration_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
802 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TOFCalibration_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TOFCalibration_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TOFCalibration_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
803 TextExporter -test -in TextExporter_1_input.featureXML -no_progress -out TextExporter_1_output.tmp > TOPP_TextExporter_1.stdout 2> TOPP_TextExporter_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
804 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
805 TextExporter -test -in TextExporter_2_input.consensusXML -ini TextExporter_2_parameters.ini > TOPP_TextExporter_2.stdout 2> TOPP_TextExporter_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
806 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
807 TextExporter -test -in TextExporter_3_input.idXML -no_progress -out TextExporter_3_output.tmp > TOPP_TextExporter_3.stdout 2> TOPP_TextExporter_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
808 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
809 TextExporter -test -in TextExporter_3_input.idXML -no_progress -out TextExporter_4_output.tmp -id:proteins_only > TOPP_TextExporter_4.stdout 2> TOPP_TextExporter_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
810 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
811 TextExporter -test -in TextExporter_5_input.idXML -no_progress -out TextExporter_5_output.tmp -id:peptides_only -id:first_dim_rt > TOPP_TextExporter_5.stdout 2> TOPP_TextExporter_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
812 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
813 TextExporter -test -in TextExporter_6_input.featureXML -no_progress -out TextExporter_6_output.tmp -no_ids > TOPP_TextExporter_6.stdout 2> TOPP_TextExporter_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
814 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
815 TextExporter -test -in TextExporter_7_input.consensusXML -ini TextExporter_7_parameters.ini > TOPP_TextExporter_7.stdout 2> TOPP_TextExporter_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
816 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
817 TextExporter -test -in TextExporter_1_input.featureXML -no_ids -no_progress -out TextExporter_8_output.tmp > TOPP_TextExporter_8.stdout 2> TOPP_TextExporter_8.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
818 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_8.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
819 TextExporter -test -in TextExporter_9_input.idXML -no_progress -out TextExporter_9_output.tmp -id:add_metavalues 0 -id:add_hit_metavalues 0 > TOPP_TextExporter_9.stdout 2> TOPP_TextExporter_9.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
820 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_9.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
821 FeatureLinkerLabeled -test -ini FeatureLinkerLabeled_1_parameters.ini -in FeatureLinkerLabeled_1_input.featureXML -out FeatureLinkerLabeled_1_output.tmp > TOPP_FeatureLinkerLabeled_1.stdout 2> TOPP_FeatureLinkerLabeled_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
822 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerLabeled_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerLabeled_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerLabeled_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
823 FeatureLinkerLabeled -test -ini FeatureLinkerLabeled_2_parameters.ini -in FeatureLinkerLabeled_2_input.featureXML -out FeatureLinkerLabeled_2_output.tmp > TOPP_FeatureLinkerLabeled_2.stdout 2> TOPP_FeatureLinkerLabeled_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
824 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerLabeled_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerLabeled_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerLabeled_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
825 FeatureLinkerUnlabeled -test -ini FeatureLinkerUnlabeled_1_parameters.ini -in FeatureLinkerUnlabeled_1_input1.featureXML FeatureLinkerUnlabeled_1_input2.featureXML FeatureLinkerUnlabeled_1_input3.featureXML -out FeatureLinkerUnlabeled_1_output.tmp > TOPP_FeatureLinkerUnlabeled_1.stdout 2> TOPP_FeatureLinkerUnlabeled_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
826 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeled_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeled_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeled_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
827 FeatureLinkerUnlabeled -test -ini FeatureLinkerUnlabeled_2_parameters.ini -in FeatureLinkerUnlabeled_2_input1.featureXML FeatureLinkerUnlabeled_2_input2.featureXML FeatureLinkerUnlabeled_2_input3.featureXML -out FeatureLinkerUnlabeled_2_output.tmp > TOPP_FeatureLinkerUnlabeled_2.stdout 2> TOPP_FeatureLinkerUnlabeled_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
828 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeled_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeled_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeled_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
829 FeatureLinkerUnlabeled -test -ini FeatureLinkerUnlabeled_3_parameters.ini -in FeatureLinkerUnlabeled_3_input1.featureXML FeatureLinkerUnlabeled_3_input2.featureXML -out FeatureLinkerUnlabeled_3_output.tmp > TOPP_FeatureLinkerUnlabeled_3.stdout 2> TOPP_FeatureLinkerUnlabeled_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
830 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeled_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeled_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeled_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
831 FeatureLinkerUnlabeled -test -ini FeatureLinkerUnlabeled_4_parameters.ini -in FeatureLinkerUnlabeled_1_input1.featureXML FeatureLinkerUnlabeled_1_input2.featureXML FeatureLinkerUnlabeled_1_input3.featureXML -out FeatureLinkerUnlabeled_4_output.tmp > TOPP_FeatureLinkerUnlabeled_4.stdout 2> TOPP_FeatureLinkerUnlabeled_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
832 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeled_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeled_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeled_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
833 FeatureLinkerUnlabeledQT -test -ini FeatureLinkerUnlabeledQT_1_parameters.ini -in FeatureLinkerUnlabeled_1_input1.featureXML FeatureLinkerUnlabeled_1_input2.featureXML FeatureLinkerUnlabeled_1_input3.featureXML -out FeatureLinkerUnlabeledQT_1_output.tmp > TOPP_FeatureLinkerUnlabeledQT_1.stdout 2> TOPP_FeatureLinkerUnlabeledQT_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
834 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledQT_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledQT_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledQT_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
835 FeatureLinkerUnlabeledQT -test -ini FeatureLinkerUnlabeledQT_2_parameters.ini -in FeatureLinkerUnlabeledQT_1_output.consensusXML FeatureLinkerUnlabeledQT_1_output.consensusXML -out FeatureLinkerUnlabeledQT_2_output.tmp > TOPP_FeatureLinkerUnlabeledQT_2.stdout 2> TOPP_FeatureLinkerUnlabeledQT_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
836 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledQT_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledQT_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledQT_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
837 FeatureLinkerUnlabeledQT -test -ini FeatureLinkerUnlabeledQT_3_parameters.ini -in FeatureLinkerUnlabeledQT_3_input1.featureXML FeatureLinkerUnlabeledQT_3_input2.featureXML -out FeatureLinkerUnlabeledQT_3_output.tmp > TOPP_FeatureLinkerUnlabeledQT_3.stdout 2> TOPP_FeatureLinkerUnlabeledQT_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
838 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledQT_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledQT_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledQT_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
839 FeatureLinkerUnlabeledQT -test -ini FeatureLinkerUnlabeledQT_1_parameters.ini -in FeatureLinkerUnlabeled_1_input1.featureXML FeatureLinkerUnlabeled_1_input2.featureXML FeatureLinkerUnlabeled_1_input3.featureXML -out FeatureLinkerUnlabeledQT_4_output.tmp -algorithm:use_identifications > TOPP_FeatureLinkerUnlabeledQT_4.stdout 2> TOPP_FeatureLinkerUnlabeledQT_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
840 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledQT_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledQT_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledQT_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
841 FeatureLinkerUnlabeledQT -test -ini FeatureLinkerUnlabeledQT_1_parameters.ini -in FeatureLinkerUnlabeledQT_5_input1.featureXML FeatureLinkerUnlabeledQT_5_input2.featureXML FeatureLinkerUnlabeledQT_5_input3.featureXML -out FeatureLinkerUnlabeledQT_5_output.tmp -algorithm:distance_RT:max_difference 200 > TOPP_FeatureLinkerUnlabeledQT_5.stdout 2> TOPP_FeatureLinkerUnlabeledQT_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
842 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledQT_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledQT_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledQT_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
843 FeatureLinkerUnlabeledQT -test -in FeatureLinkerUnlabeledQT_5_input1.featureXML FeatureLinkerUnlabeledQT_5_input2.featureXML FeatureLinkerUnlabeledQT_5_input3.featureXML -out FeatureLinkerUnlabeledQT_6_output.tmp -algorithm:use_identifications -algorithm:distance_RT:max_difference 200 > TOPP_FeatureLinkerUnlabeledQT_6.stdout 2> TOPP_FeatureLinkerUnlabeledQT_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
844 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledQT_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledQT_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledQT_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
845 FeatureLinkerUnlabeledKD -test -ini FeatureLinkerUnlabeledKD_1_parameters.ini -in FeatureLinkerUnlabeled_1_input1.featureXML FeatureLinkerUnlabeled_1_input2.featureXML FeatureLinkerUnlabeled_1_input3.featureXML -out FeatureLinkerUnlabeledKD_1_output.tmp > TOPP_FeatureLinkerUnlabeledKD_1.stdout 2> TOPP_FeatureLinkerUnlabeledKD_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
846 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledKD_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledKD_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledKD_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
847 FeatureLinkerUnlabeledKD -test -ini FeatureLinkerUnlabeledKD_2_parameters.ini -in FeatureLinkerUnlabeledKD_1_output.consensusXML FeatureLinkerUnlabeledKD_1_output.consensusXML -out FeatureLinkerUnlabeledKD_2_output.tmp > TOPP_FeatureLinkerUnlabeledKD_2.stdout 2> TOPP_FeatureLinkerUnlabeledKD_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
848 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledKD_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledKD_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledKD_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
849 FeatureLinkerUnlabeledKD -test -ini FeatureLinkerUnlabeledKD_3_parameters.ini -in FeatureLinkerUnlabeledQT_3_input1.featureXML FeatureLinkerUnlabeledQT_3_input2.featureXML -out FeatureLinkerUnlabeledKD_3_output.tmp > TOPP_FeatureLinkerUnlabeledKD_3.stdout 2> TOPP_FeatureLinkerUnlabeledKD_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
850 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledKD_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledKD_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledKD_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
851 FeatureLinkerUnlabeledKD -test -ini FeatureLinkerUnlabeledKD_4_parameters.ini -in FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML FeatureLinkerUnlabeledKD_dc_input3.featureXML FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML -out FeatureLinkerUnlabeledKD_4_output.tmp -algorithm:link:charge_merging Identical -algorithm:link:adduct_merging Any > TOPP_FeatureLinkerUnlabeledKD_4.stdout 2> TOPP_FeatureLinkerUnlabeledKD_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
852 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledKD_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledKD_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledKD_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
853 FeatureLinkerUnlabeledKD -test -ini FeatureLinkerUnlabeledKD_4_parameters.ini -in FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML FeatureLinkerUnlabeledKD_dc_input3.featureXML FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML -out FeatureLinkerUnlabeledKD_5_output.tmp -algorithm:link:charge_merging With_charge_zero -algorithm:link:adduct_merging Any > TOPP_FeatureLinkerUnlabeledKD_5.stdout 2> TOPP_FeatureLinkerUnlabeledKD_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
854 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledKD_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledKD_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledKD_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
855 FeatureLinkerUnlabeledKD -test -ini FeatureLinkerUnlabeledKD_4_parameters.ini -in FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML FeatureLinkerUnlabeledKD_dc_input3.featureXML FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML -out FeatureLinkerUnlabeledKD_6_output.tmp -algorithm:link:charge_merging Any -algorithm:link:adduct_merging With_unknown_adducts > TOPP_FeatureLinkerUnlabeledKD_6.stdout 2> TOPP_FeatureLinkerUnlabeledKD_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
856 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledKD_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledKD_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledKD_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
857 FeatureLinkerUnlabeledKD -test -ini FeatureLinkerUnlabeledKD_4_parameters.ini -in FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML FeatureLinkerUnlabeledKD_dc_input3.featureXML FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML -out FeatureLinkerUnlabeledKD_7_output.tmp -algorithm:link:charge_merging Any -algorithm:link:adduct_merging Identical > TOPP_FeatureLinkerUnlabeledKD_7.stdout 2> TOPP_FeatureLinkerUnlabeledKD_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
858 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledKD_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledKD_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledKD_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
859 IDMapper -test -in IDMapper_1_input.featureXML -out IDMapper_1_output.tmp -id IDMapper_1_input.idXML -mz_measure Da -mz_tolerance 1 -ignore_charge -mz_reference precursor -feature:use_centroid_mz false > TOPP_IDMapper_1.stdout 2> TOPP_IDMapper_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
860 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMapper_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMapper_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMapper_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
861 IDMapper -test -in IDMapper_2_input.consensusXML -out IDMapper_2_output.tmp -id IDMapper_2_input.idXML -mz_measure Da -mz_tolerance 1 -mz_reference precursor > TOPP_IDMapper_2.stdout 2> TOPP_IDMapper_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
862 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMapper_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMapper_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMapper_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
863 IDMapper -test -in IDMapper_3_input.featureXML -out IDMapper_3_output.tmp -id IDMapper_3_input.idXML -mz_measure ppm -mz_tolerance 3 -rt_tolerance 4 -ignore_charge -mz_reference precursor > TOPP_IDMapper_3.stdout 2> TOPP_IDMapper_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
864 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMapper_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMapper_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMapper_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
865 IDMapper -test -in IDMapper_4_input.featureXML -out IDMapper_4_output.tmp -id IDMapper_4_input.idXML -spectra:in IDMapper_4_input.mzML -mz_measure ppm -mz_tolerance 20 -rt_tolerance 10 > TOPP_IDMapper_4.stdout 2> TOPP_IDMapper_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
866 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMapper_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMapper_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMapper_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
867 IDMapper -test -in IDMapper_5_input.featureXML -out IDMapper_5_output.tmp -id IDMapper_5_input.idXML -spectra:in IDMapper_5_input.mzML -mz_measure ppm -mz_tolerance 10 -rt_tolerance 20 -feature:use_centroid_mz false > TOPP_IDMapper_5.stdout 2> TOPP_IDMapper_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
868 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMapper_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMapper_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMapper_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
869 IDRipper -test -in IDRipper_1_input.idXML -out dummy.tmp > TOPP_IDRipper_1.stdout 2> TOPP_IDRipper_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
870 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDRipper_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDRipper_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDRipper_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
871 IDRipper -test -in IDRipper_2_input.idXML -out_path dummy.tmp > TOPP_IDRipper_2.stdout 2> TOPP_IDRipper_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
872 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDRipper_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDRipper_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDRipper_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
873 IDMerger -test -in IDRipper_3_input1.idXML IDRipper_3_input2.idXML -out IDRipper_3_output.tmp -annotate_file_origin > TOPP_IDRipper_3_prep.stdout 2> TOPP_IDRipper_3_prep.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
874 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDRipper_3_prep failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDRipper_3_prep.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDRipper_3_prep.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
875 IDRipper -test -in IDRipper_3_output.idXML -out_path dummy2.tmp > TOPP_IDRipper_3.stdout 2> TOPP_IDRipper_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
876 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDRipper_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDRipper_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDRipper_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
877 ConsensusID -test -in ConsensusID_1_input.idXML -out ConsensusID_1_output.tmp -algorithm PEPMatrix -PEPMatrix:matrix PAM30MS > TOPP_ConsensusID_1.stdout 2> TOPP_ConsensusID_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
878 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusID_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusID_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConsensusID_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
879 ConsensusID -test -in ConsensusID_2_input.featureXML -out ConsensusID_2_output.tmp -algorithm average > TOPP_ConsensusID_2.stdout 2> TOPP_ConsensusID_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
880 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusID_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusID_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConsensusID_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
881 ConsensusID -test -in ConsensusID_3_input.consensusXML -out ConsensusID_3_output.tmp -algorithm best > TOPP_ConsensusID_3.stdout 2> TOPP_ConsensusID_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
882 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusID_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusID_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConsensusID_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
883 ConsensusID -test -in ConsensusID_1_input.idXML -out ConsensusID_4_output.tmp -algorithm PEPMatrix -PEPMatrix:matrix identity -filter:considered_hits 6 > TOPP_ConsensusID_4.stdout 2> TOPP_ConsensusID_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
884 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusID_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusID_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConsensusID_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
885 ConsensusID -test -in ConsensusID_1_input.idXML -out ConsensusID_5_output.tmp -algorithm PEPIons > TOPP_ConsensusID_5.stdout 2> TOPP_ConsensusID_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
886 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusID_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusID_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConsensusID_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
887 ConsensusID -test -in ConsensusID_1_input.idXML -out ConsensusID_6_output.tmp -algorithm best -filter:min_support 0.5 > TOPP_ConsensusID_6.stdout 2> TOPP_ConsensusID_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
888 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusID_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusID_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConsensusID_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
889 PrecursorIonSelector -test -in PrecursorIonSelector_features.featureXML -sim_results PrecursorIonSelector_1_output.tmp -ini PrecursorIonSelector_1_parameters.ini -db_path PrecursorIonSelector_db.fasta -ids PrecursorIonSelector_ids.idXML > TOPP_PrecursorIonSelector_1.stdout 2> TOPP_PrecursorIonSelector_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
890 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PrecursorIonSelector_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PrecursorIonSelector_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PrecursorIonSelector_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
891 PrecursorIonSelector -test -in PrecursorIonSelector_features.featureXML -out PrecursorIonSelector_2_output.tmp -ini PrecursorIonSelector_2_parameters.ini -db_path PrecursorIonSelector_db.fasta -ids PrecursorIonSelector_ids.idXML > TOPP_PrecursorIonSelector_2.stdout 2> TOPP_PrecursorIonSelector_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
892 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PrecursorIonSelector_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PrecursorIonSelector_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PrecursorIonSelector_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
893 CompNovo -test -in CompNovo_1_input.mzML -ini CompNovo_1.ini -out CompNovo_1_output.tmp > TOPP_CompNovo_1.stdout 2> TOPP_CompNovo_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
894 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_CompNovo_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_CompNovo_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_CompNovo_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
895 CompNovoCID -test -in CompNovoCID_1_input.mzML -ini CompNovoCID_1.ini -out CompNovoCID_1_output.tmp > TOPP_CompNovoCID_1.stdout 2> TOPP_CompNovoCID_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
896 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_CompNovoCID_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_CompNovoCID_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_CompNovoCID_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
897 PrecursorMassCorrector -test -in PrecursorMassCorrector_1_input.mzML -ini PrecursorMassCorrector_1.ini -out PrecursorMassCorrector_1_output.tmp > TOPP_PrecursorMassCorrector_1.stdout 2> TOPP_PrecursorMassCorrector_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
898 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PrecursorMassCorrector_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PrecursorMassCorrector_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PrecursorMassCorrector_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
899 FalseDiscoveryRate -test -in FalseDiscoveryRate_OMSSA.idXML -out FalseDiscoveryRate_output_1.tmp -PSM true -protein false > TOPP_FalseDiscoveryRate_1.stdout 2> TOPP_FalseDiscoveryRate_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
900 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FalseDiscoveryRate_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FalseDiscoveryRate_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FalseDiscoveryRate_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
901 FalseDiscoveryRate -test -in FalseDiscoveryRate_OMSSA.idXML -out FalseDiscoveryRate_output_2.tmp -algorithm:treat_runs_separately -PSM true -protein false > TOPP_FalseDiscoveryRate_2.stdout 2> TOPP_FalseDiscoveryRate_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
902 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FalseDiscoveryRate_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FalseDiscoveryRate_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FalseDiscoveryRate_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
903 FalseDiscoveryRate -test -in FalseDiscoveryRate_OMSSA.idXML -out FalseDiscoveryRate_output_3.tmp -algorithm:split_charge_variants -PSM true -protein false > TOPP_FalseDiscoveryRate_3.stdout 2> TOPP_FalseDiscoveryRate_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
904 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FalseDiscoveryRate_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FalseDiscoveryRate_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FalseDiscoveryRate_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
905 FalseDiscoveryRate -test -in FalseDiscoveryRate_OMSSA_4.idXML -out FalseDiscoveryRate_output_4.tmp -algorithm:split_charge_variants -PSM true -protein false > TOPP_FalseDiscoveryRate_4.stdout 2> TOPP_FalseDiscoveryRate_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
906 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FalseDiscoveryRate_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FalseDiscoveryRate_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FalseDiscoveryRate_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
907 FalseDiscoveryRate -test -in FalseDiscoveryRate_5_input.idXML -out FalseDiscoveryRate_5_output.tmp -PSM false -protein true -algorithm:add_decoy_proteins -force > TOPP_FalseDiscoveryRate_5.stdout 2> TOPP_FalseDiscoveryRate_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
908 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FalseDiscoveryRate_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FalseDiscoveryRate_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FalseDiscoveryRate_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
909 FalseDiscoveryRate -test -in FalseDiscoveryRate_6_input.idXML -out FalseDiscoveryRate_6_output.tmp -PSM true -protein false -FDR:PSM 0.05 > TOPP_FalseDiscoveryRate_6.stdout 2> TOPP_FalseDiscoveryRate_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
910 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FalseDiscoveryRate_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FalseDiscoveryRate_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FalseDiscoveryRate_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
911 FalseDiscoveryRate -test -in FalseDiscoveryRate_7_input.idXML -out FalseDiscoveryRate_7_output.tmp -PSM false -protein true -FDR:protein 0.30 -force > TOPP_FalseDiscoveryRate_7.stdout 2> TOPP_FalseDiscoveryRate_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
912 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FalseDiscoveryRate_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FalseDiscoveryRate_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FalseDiscoveryRate_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
913 IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_Mascot_input.idXML -out IDPosteriorErrorProbability_output_1.tmp > TOPP_IDPosteriorErrorProbability_1.stdout 2> TOPP_IDPosteriorErrorProbability_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
914 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
915 IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_XTandem_input.idXML -out IDPosteriorErrorProbability_output_2.tmp > TOPP_IDPosteriorErrorProbability_2.stdout 2> TOPP_IDPosteriorErrorProbability_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
916 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
917 IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_OMSSA_input.idXML -out IDPosteriorErrorProbability_output_3.tmp > TOPP_IDPosteriorErrorProbability_3.stdout 2> TOPP_IDPosteriorErrorProbability_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
918 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
919 IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_OMSSA_input2.idXML -out IDPosteriorErrorProbability_output_4.tmp -split_charge > TOPP_IDPosteriorErrorProbability_4.stdout 2> TOPP_IDPosteriorErrorProbability_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
920 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
921 IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_XTandem_input2.idXML -out IDPosteriorErrorProbability_output_5.tmp -split_charge > TOPP_IDPosteriorErrorProbability_5.stdout 2> TOPP_IDPosteriorErrorProbability_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
922 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
923 IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_Mascot_input2.idXML -out IDPosteriorErrorProbability_output_6.tmp -split_charge > TOPP_IDPosteriorErrorProbability_6.stdout 2> TOPP_IDPosteriorErrorProbability_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
924 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
925 IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_bad_data.idXML -out IDPosteriorErrorProbability_bad_data_output.tmp -ignore_bad_data > TOPP_IDPosteriorErrorProbability_7.stdout 2> TOPP_IDPosteriorErrorProbability_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
926 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
927 IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_OMSSA_input.idXML -out IDPosteriorErrorProbability_output_8.tmp -prob_correct > TOPP_IDPosteriorErrorProbability_8.stdout 2> TOPP_IDPosteriorErrorProbability_8.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
928 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_8.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
929 ProteinResolver -test -in ProteinResolver_1_input.consensusXML -fasta ProteinResolver_1_input.fasta -protein_groups ProteinResolver_1_output1.tmp -peptide_table ProteinResolver_1_output2.tmp -protein_table ProteinResolver_1_output3.tmp > TOPP_ProteinResolver_1.stdout 2> TOPP_ProteinResolver_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
930 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinResolver_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinResolver_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinResolver_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
931 ProteinQuantifier -test -in ProteinQuantifier_input.featureXML -out ProteinQuantifier_1_output1.tmp -peptide_out ProteinQuantifier_1_output2.tmp > TOPP_ProteinQuantifier_1.stdout 2> TOPP_ProteinQuantifier_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
932 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
933 ProteinQuantifier -test -in ProteinQuantifier_input.featureXML -out ProteinQuantifier_2_output1.tmp -peptide_out ProteinQuantifier_2_output2.tmp -top 2 -include_all -best_charge_and_fraction -average sum > TOPP_ProteinQuantifier_2.stdout 2> TOPP_ProteinQuantifier_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
934 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
935 ProteinQuantifier -test -in ProteinQuantifier_3_input.featureXML -out ProteinQuantifier_3_output1.tmp -peptide_out ProteinQuantifier_3_output2.tmp -top 2 -include_all -average mean > TOPP_ProteinQuantifier_3.stdout 2> TOPP_ProteinQuantifier_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
936 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
937 ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_4_output.tmp -top 0 -average sum > TOPP_ProteinQuantifier_4.stdout 2> TOPP_ProteinQuantifier_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
938 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
939 ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_5_output.tmp -top 3 -average sum > TOPP_ProteinQuantifier_5.stdout 2> TOPP_ProteinQuantifier_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
940 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
941 ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_6_output.tmp -top 3 -include_all -average sum > TOPP_ProteinQuantifier_6.stdout 2> TOPP_ProteinQuantifier_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
942 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
943 ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_7_output.tmp -top 0 -consensus:fix_peptides -average sum > TOPP_ProteinQuantifier_7.stdout 2> TOPP_ProteinQuantifier_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
944 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
945 ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_8_output.tmp -top 3 -consensus:fix_peptides -average sum > TOPP_ProteinQuantifier_8.stdout 2> TOPP_ProteinQuantifier_8.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
946 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_8.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
947 ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_9_output.tmp -top 3 -include_all -consensus:fix_peptides -average sum > TOPP_ProteinQuantifier_9.stdout 2> TOPP_ProteinQuantifier_9.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
948 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_9.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
949 ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_12_output.tmp -top 3 -include_all -consensus:fix_peptides -average sum -ratios > TOPP_ProteinQuantifier_12.stdout 2> TOPP_ProteinQuantifier_12.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
950 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_12.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
951 ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_13_output.tmp -top 3 -include_all -consensus:fix_peptides -average sum -ratiosSILAC > TOPP_ProteinQuantifier_13.stdout 2> TOPP_ProteinQuantifier_13.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
952 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_13.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
953 ProteinQuantifier -test -in ProteinQuantifier_input.idXML -out ProteinQuantifier_14_output1.tmp -peptide_out ProteinQuantifier_14_output2.tmp -top 0 -average sum > TOPP_ProteinQuantifier_14.stdout 2> TOPP_ProteinQuantifier_14.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
954 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_14.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
955 InclusionExclusionListCreator -test -include InclusionExclusionListCreator.featureXML -out InclusionExclusionListCreator_1_output.tmp > TOPP_InclusionExclusionListCreator_1.stdout 2> TOPP_InclusionExclusionListCreator_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
956 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InclusionExclusionListCreator_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InclusionExclusionListCreator_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InclusionExclusionListCreator_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
957 InclusionExclusionListCreator -test -exclude InclusionExclusionListCreator.featureXML -out InclusionExclusionListCreator_2_output.tmp -ini InclusionExclusionListCreator_2.ini > TOPP_InclusionExclusionListCreator_2.stdout 2> TOPP_InclusionExclusionListCreator_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
958 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InclusionExclusionListCreator_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InclusionExclusionListCreator_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InclusionExclusionListCreator_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
959 InclusionExclusionListCreator -test -include InclusionExclusionListCreator.fasta -out InclusionExclusionListCreator_3_output.tmp -inclusion_charges 1 2 -rt_model InclusionExclusionListCreator_rt.model > TOPP_InclusionExclusionListCreator_3.stdout 2> TOPP_InclusionExclusionListCreator_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
960 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InclusionExclusionListCreator_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InclusionExclusionListCreator_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InclusionExclusionListCreator_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
961 InclusionExclusionListCreator -test -exclude InclusionExclusionListCreator.fasta -out InclusionExclusionListCreator_4_output.tmp -exclusion_charges 1 2 -rt_model InclusionExclusionListCreator_rt.model -ini InclusionExclusionListCreator_4.ini > TOPP_InclusionExclusionListCreator_4.stdout 2> TOPP_InclusionExclusionListCreator_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
962 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InclusionExclusionListCreator_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InclusionExclusionListCreator_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InclusionExclusionListCreator_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
963 InclusionExclusionListCreator -test -exclude InclusionExclusionListCreator.idXML -out InclusionExclusionListCreator_5_output.tmp -exclusion_charges 1 2 -rt_model InclusionExclusionListCreator_rt.model > TOPP_InclusionExclusionListCreator_5.stdout 2> TOPP_InclusionExclusionListCreator_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
964 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InclusionExclusionListCreator_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InclusionExclusionListCreator_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InclusionExclusionListCreator_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
965 InclusionExclusionListCreator -test -exclude InclusionExclusionListCreator.idXML -out InclusionExclusionListCreator_6_output.tmp -exclusion_charges 1 2 -rt_model InclusionExclusionListCreator_rt.model -ini InclusionExclusionListCreator_6.ini > TOPP_InclusionExclusionListCreator_6.stdout 2> TOPP_InclusionExclusionListCreator_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
966 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InclusionExclusionListCreator_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InclusionExclusionListCreator_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InclusionExclusionListCreator_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
967 PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_1.idXML -out PeptideIndexer_1_out.tmp.idXML -allow_unmatched -enzyme:specificity none -aaa_max 4 > TOPP_PeptideIndexer_1.stdout 2> TOPP_PeptideIndexer_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
968 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
969 PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_1.idXML -out PeptideIndexer_2_out.tmp.idXML -allow_unmatched -write_protein_sequence -enzyme:specificity none -aaa_max 4 > TOPP_PeptideIndexer_2.stdout 2> TOPP_PeptideIndexer_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
970 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
971 PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_1.idXML -out PeptideIndexer_3_out.tmp.idXML -allow_unmatched -keep_unreferenced_proteins -enzyme:specificity none -aaa_max 4 > TOPP_PeptideIndexer_3.stdout 2> TOPP_PeptideIndexer_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
972 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
973 PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_1.idXML -out PeptideIndexer_4_out.tmp.idXML -allow_unmatched -aaa_max 0 -write_protein_sequence -enzyme:specificity none -aaa_max 4 > TOPP_PeptideIndexer_4.stdout 2> TOPP_PeptideIndexer_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
974 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
975 PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_1.idXML -out PeptideIndexer_5_out.tmp.idXML -allow_unmatched -enzyme:specificity none -aaa_max 4 > TOPP_PeptideIndexer_5.stdout 2> TOPP_PeptideIndexer_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
976 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
977 PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_2.idXML -out PeptideIndexer_6_out.tmp.idXML -allow_unmatched -enzyme:specificity none -aaa_max 3 > TOPP_PeptideIndexer_6.stdout 2> TOPP_PeptideIndexer_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
978 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
979 PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_3.idXML -out PeptideIndexer_7_out.tmp.idXML -allow_unmatched -aaa_max 4 -decoy_string DECOY_ > TOPP_PeptideIndexer_7.stdout 2> TOPP_PeptideIndexer_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
980 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
981 PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_3.idXML -out PeptideIndexer_8_out.tmp.idXML -allow_unmatched -enzyme:specificity semi -aaa_max 4 > TOPP_PeptideIndexer_8.stdout 2> TOPP_PeptideIndexer_8.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
982 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_8.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
983 PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_3.idXML -out PeptideIndexer_9_out.tmp.idXML -allow_unmatched -enzyme:specificity none -aaa_max 4 > TOPP_PeptideIndexer_9.stdout 2> TOPP_PeptideIndexer_9.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
984 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_9.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
985 PeptideIndexer -test -fasta PeptideIndexer_10_input.fasta -in PeptideIndexer_10_input.idXML -out PeptideIndexer_10_output.tmp.idXML -IL_equivalent -aaa_max 3 -write_protein_sequence > TOPP_PeptideIndexer_10.stdout 2> TOPP_PeptideIndexer_10.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
986 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_10.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
987 PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_1.idXML -out PeptideIndexer_12_out.tmp.idXML -allow_unmatched -enzyme:specificity none -aaa_max 4 > TOPP_PeptideIndexer_12.stdout 2> TOPP_PeptideIndexer_12.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
988 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_12.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
989 PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in empty.idXML -out PeptideIndexer_13_out.tmp.idXML -aaa_max 4 > TOPP_PeptideIndexer_13.stdout 2> TOPP_PeptideIndexer_13.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
990 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_13.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
991 PeptideIndexer -test -fasta PeptideIndexer_2.fasta -in PeptideIndexer_14.idXML -out PeptideIndexer_14_out.tmp.idXML -enzyme:specificity none -aaa_max 4 -write_protein_sequence > TOPP_PeptideIndexer_14.stdout 2> TOPP_PeptideIndexer_14.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
992 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_14.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
993 MzTabExporter -test -in MzTabExporter_1_input.consensusXML -out MzTabExporter_1_output.tmp > TOPP_MzTabExporter_1.stdout 2> TOPP_MzTabExporter_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
994 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MzTabExporter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MzTabExporter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MzTabExporter_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
995 MzTabExporter -test -in MzTabExporter_2_input.idXML -out MzTabExporter_2_output.tmp > TOPP_MzTabExporter_2.stdout 2> TOPP_MzTabExporter_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
996 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MzTabExporter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MzTabExporter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MzTabExporter_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
997 MzTabExporter -test -in MzTabExporter_3_input.featureXML -out MzTabExporter_3_output.tmp > TOPP_MzTabExporter_3.stdout 2> TOPP_MzTabExporter_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
998 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MzTabExporter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MzTabExporter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MzTabExporter_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
999 OpenPepXL -test -decoy_string "decoy" -in OpenPepXL_input.mzML -consensus OpenPepXL_input.consensusXML -database OpenPepXL_input.fasta -out_xquestxml OpenPepXL_output.xquest.xml.tmp -out_xquest_specxml OpenPepXL_output.spec.xml.tmp -out_mzIdentML OpenPepXL_output.mzid.tmp -out_idXML OpenPepXL_output.idXML.tmp > TOPP_OpenPepXL_1.stdout 2> TOPP_OpenPepXL_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1000 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenPepXL_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenPepXL_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenPepXL_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1001 OpenPepXLLF -test -decoy_string "decoy" -in OpenPepXLLF_input.mzML -database OpenPepXLLF_input.fasta -out_xquestxml OpenPepXLLF_output.xquest.xml.tmp -out_xquest_specxml OpenPepXLLF_output.spec.xml.tmp -out_mzIdentML OpenPepXLLF_output.mzid.tmp -out_idXML OpenPepXLLF_output.idXML.tmp > TOPP_OpenPepXLLF_1.stdout 2> TOPP_OpenPepXLLF_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1002 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenPepXLLF_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenPepXLLF_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenPepXLLF_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1003 OpenPepXLLF -test -ini OpenPepXLLF_input2.ini -in OpenPepXLLF_input2.mzML -database OpenPepXLLF_input2.fasta -out_idXML OpenPepXLLF_output2.idXML.tmp > TOPP_OpenPepXLLF_2.stdout 2> TOPP_OpenPepXLLF_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1004 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenPepXLLF_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenPepXLLF_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenPepXLLF_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1005 XFDR -test -binsize 0.1 -in XFDR_test_in1.idXML -out_idXML XFDR_test_out1_temp.idXML -out_mzIdentML XFDR_test_out1_temp.mzid -out_xquest XFDR_test_out1_temp.xquest.xml > TOPP_XFDR_1.stdout 2> TOPP_XFDR_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1006 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XFDR_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XFDR_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XFDR_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1007 XFDR -test -binsize 0.1 -in XFDR_test_in1.idXML -uniquexl -no_qvalues -out_idXML XFDR_test_out2_temp.idXML -out_mzIdentML XFDR_test_out2_temp.mzid -out_xquest XFDR_test_out2_temp.xquest.xml > TOPP_XFDR_2.stdout 2> TOPP_XFDR_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1008 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XFDR_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XFDR_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XFDR_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1009 XFDR -test -binsize 0.1 -minscore 0.0 -in XFDR_test_in2.xquest.xml -out_idXML XFDR_test_out3_temp.idXML -out_mzIdentML XFDR_test_out3_temp.mzid -out_xquest XFDR_test_out3_temp.xquest.xml > TOPP_XFDR_3.stdout 2> TOPP_XFDR_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1010 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XFDR_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XFDR_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XFDR_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1011 XFDR -test -binsize 0.1 -minborder -3 -maxborder 3 -in XFDR_test_in2.xquest.xml -out_idXML XFDR_test_out4_temp.idXML -out_mzIdentML XFDR_test_out4_temp.mzid -out_xquest XFDR_test_out4_temp.xquest.xml > TOPP_XFDR_4.stdout 2> TOPP_XFDR_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1012 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XFDR_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XFDR_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XFDR_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1013 XFDR -test -binsize 0.1 -minborder -3 -maxborder 3 -in XFDR_test_in3.xquest.xml -out_idXML XFDR_test_out5_temp.idXML -out_mzIdentML XFDR_test_out5_temp.mzid -out_xquest XFDR_test_out5_temp.xquest.xml > TOPP_XFDR_5.stdout 2> TOPP_XFDR_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1014 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XFDR_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XFDR_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XFDR_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1015 XFDR -test -binsize 0.1 -in XFDR_test_in4.idXML -out_idXML XFDR_test_out6_temp.idXML > TOPP_XFDR_6.stdout 2> TOPP_XFDR_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1016 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XFDR_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XFDR_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XFDR_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1017 XFDR -test -uniquexl -binsize 0.1 -minscore 0.0 -in XFDR_test_in2.xquest.xml -out_idXML XFDR_test_out7_temp.idXML -out_mzIdentML XFDR_test_out7_temp.mzid -out_xquest XFDR_test_out7_temp.xquest.xml > TOPP_XFDR_7.stdout 2> TOPP_XFDR_7.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1018 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XFDR_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XFDR_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XFDR_7.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1019 QualityControl -test -in_raw QualityControl_1_in1.mzML.gz QualityControl_1_in2.mzML.gz QualityControl_1_in3.mzML.gz -in_postFDR QualityControl_1_in1.featureXML QualityControl_1_in2.featureXML QualityControl_1_in3.featureXML -in_trafo QualityControl_1_in1.trafoXML QualityControl_1_in2.trafoXML QualityControl_1_in3.trafoXML -in_contaminants QualityControl_1.fasta -in_cm QualityControl_1_in.consensusXML -out_cm QualityControl_1_out.consensusXML.tmp -out QualityControl_1_out.mzTab.tmp > TOPP_QualityControl_1.stdout 2> TOPP_QualityControl_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1020 if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_QualityControl_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_QualityControl_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_QualityControl_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1021 AccurateMassSearch -test -in ConsensusMapNormalizer_input.consensusXML -out AccurateMassSearch_1_output.tmp.mzTab > UTILS_AccurateMassSearch_1.stdout 2> UTILS_AccurateMassSearch_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1022 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AccurateMassSearch_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AccurateMassSearch_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AccurateMassSearch_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1023 AccurateMassSearch -test -in AccurateMassSearch_2_input.featureXML -out AccurateMassSearch_2_output.tmp.mzTab -out_annotation AccurateMassSearch_2_output.tmp.featureXML -db:mapping AMS_test_Mapping.tsv -db:struct AMS_test_Struct.tsv -positive_adducts AMS_PositiveAdducts.tsv -negative_adducts AMS_NegativeAdducts.tsv -algorithm:mzTab:exportIsotopeIntensities true > UTILS_AccurateMassSearch_2.stdout 2> UTILS_AccurateMassSearch_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1024 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AccurateMassSearch_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AccurateMassSearch_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AccurateMassSearch_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1025 AccurateMassSearch -test -in AccurateMassSearch_2_input.featureXML -out AccurateMassSearch_3_output.tmp.mzTab -out_annotation AccurateMassSearch_2_output.tmp.featureXML -db:mapping AMS_test_Mapping.tsv -db:struct AMS_test_Struct.tsv -positive_adducts AMS_PositiveAdducts.tsv -negative_adducts AMS_NegativeAdducts.tsv > UTILS_AccurateMassSearch_3.stdout 2> UTILS_AccurateMassSearch_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1026 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AccurateMassSearch_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AccurateMassSearch_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AccurateMassSearch_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1027 AssayGeneratorMetabo -test -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ffm_input.featureXML -out AssayGeneratorMetabo_ffm_output.tmp.tsv -min_transitions 1 > UTILS_AssayGeneratorMetabo_1.stdout 2> UTILS_AssayGeneratorMetabo_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1028 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1029 AssayGeneratorMetabo -test -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ams_input.featureXML -out AssayGeneratorMetabo_ams_output.tmp.tsv -min_transitions 1 > UTILS_AssayGeneratorMetabo_2.stdout 2> UTILS_AssayGeneratorMetabo_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1030 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1031 AssayGeneratorMetabo -test -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ffm_input.featureXML -out AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv -method consensus_spectrum -min_transitions 1 > UTILS_AssayGeneratorMetabo_3.stdout 2> UTILS_AssayGeneratorMetabo_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1032 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1033 AssayGeneratorMetabo -test -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ams_input.featureXML -out AssayGeneratorMetabo_ams_output_consensus.tmp.tsv -method consensus_spectrum -min_transitions 1 > UTILS_AssayGeneratorMetabo_4.stdout 2> UTILS_AssayGeneratorMetabo_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1034 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_4 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1035 AssayGeneratorMetabo -test -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ams_input.featureXML -out AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv -method consensus_spectrum -use_known_unknowns -min_transitions 1 > UTILS_AssayGeneratorMetabo_5.stdout 2> UTILS_AssayGeneratorMetabo_5.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1036 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_5 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_5.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1037 TargetedFileConverter -test -in AssayGeneratorMetabo_ams_uku_output_consensus.tsv -out AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML > UTILS_AssayGeneratorMetabo_6.stdout 2> UTILS_AssayGeneratorMetabo_6.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1038 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_6 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_6.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1039 ImageCreator -test -in ImageCreator_1_input.mzML -out ImageCreator1.bmp -width 20 -height 15 > UTILS_ImageCreator_1.stdout 2> UTILS_ImageCreator_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1040 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_ImageCreator_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_ImageCreator_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_ImageCreator_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1041 ImageCreator -test -in ImageCreator_2_input.mzML -out ImageCreator2.png -out_type bmp -width 20 -height 15 -precursors -precursor_size 3 -precursor_color green -log_intensity > UTILS_ImageCreator_2.stdout 2> UTILS_ImageCreator_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1042 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_ImageCreator_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_ImageCreator_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_ImageCreator_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1043 IDScoreSwitcher -test -in IDFileConverter_12_output.idXML -out IDScoreSwitcher_1_output.tmp -new_score Percolator_PEP -new_score_type "Posterior Error Probability" -new_score_orientation lower_better -old_score Percolator_qvalue > UTILS_IDScoreSwitcher_1.stdout 2> UTILS_IDScoreSwitcher_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1044 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_IDScoreSwitcher_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_IDScoreSwitcher_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_IDScoreSwitcher_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1045 IDScoreSwitcher -test -in IDScoreSwitcher_2_input.idXML -out IDScoreSwitcher_2_output.tmp -new_score "Posterior Probability_score" -new_score_type "Posterior Probability" -new_score_orientation higher_better -proteins > UTILS_IDScoreSwitcher_2.stdout 2> UTILS_IDScoreSwitcher_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1046 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_IDScoreSwitcher_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_IDScoreSwitcher_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_IDScoreSwitcher_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1047 IDSplitter -test -in IDMapper_1_output.featureXML -out IDSplitter_1_output1.tmp -id_out IDSplitter_1_output2.tmp > UTILS_IDSplitter_1.stdout 2> UTILS_IDSplitter_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1048 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_IDSplitter_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_IDSplitter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_IDSplitter_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1049 MassCalculator -test -in MassCalculator_1_input.txt -out MassCalculator_1_output.tmp -charge 0 1 -format table -separator , > UTILS_MassCalculator_1.stdout 2> UTILS_MassCalculator_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1050 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MassCalculator_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MassCalculator_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MassCalculator_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1051 MassCalculator -test -in_seq "LDQWLC(Carbamidomethyl)EKL" "(Glu->pyro-Glu)EAM(Oxidation)APKHK" "RANVM(Oxidation)DYR" "FGVEQDVDMVFASFIR" -out MassCalculator_2_output.tmp -charge 1 2 3 > UTILS_MassCalculator_2.stdout 2> UTILS_MassCalculator_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1052 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MassCalculator_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MassCalculator_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MassCalculator_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1053 MultiplexResolver -test -in MultiplexResolver_1_input.consensusXML -ini MultiplexResolver_1_parameters.ini -out MultiplexResolver_1.tmp -out_conflicts MultiplexResolver_1_conflicts.tmp > UTILS_MultiplexResolver_1.stdout 2> UTILS_MultiplexResolver_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1054 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MultiplexResolver_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MultiplexResolver_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MultiplexResolver_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1055 MultiplexResolver -test -in MultiplexResolver_2_input.consensusXML -ini MultiplexResolver_2_parameters.ini -out MultiplexResolver_2.tmp -out_conflicts MultiplexResolver_2_conflicts.tmp > UTILS_MultiplexResolver_2.stdout 2> UTILS_MultiplexResolver_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1056 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MultiplexResolver_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MultiplexResolver_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MultiplexResolver_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1057 MultiplexResolver -test -in MultiplexResolver_3_input.consensusXML -ini MultiplexResolver_3_parameters.ini -out MultiplexResolver_3.tmp -out_conflicts MultiplexResolver_3_conflicts.tmp > UTILS_MultiplexResolver_3.stdout 2> UTILS_MultiplexResolver_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1058 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MultiplexResolver_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MultiplexResolver_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MultiplexResolver_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1059 MultiplexResolver -test -in MultiplexResolver_4_input.consensusXML -in_blacklist MultiplexResolver_4_input.mzML -ini MultiplexResolver_4_parameters.ini -out MultiplexResolver_4.tmp -out_conflicts MultiplexResolver_4_conflicts.tmp > UTILS_MultiplexResolver_4.stdout 2> UTILS_MultiplexResolver_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1060 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MultiplexResolver_4 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MultiplexResolver_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MultiplexResolver_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1061 INIUpdater -test -in INIUpdater_1_noupdate.toppas -out INIUpdater_1_noupdate.toppas.tmp > UTILS_INIUpdater_1.stdout 2> UTILS_INIUpdater_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1062 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_INIUpdater_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_INIUpdater_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_INIUpdater_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1063 INIUpdater -test -in INIUpdater_3_old.toppas -out INIUpdater_3_old.toppas.tmp > UTILS_INIUpdater_3.stdout 2> UTILS_INIUpdater_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1064 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_INIUpdater_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_INIUpdater_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_INIUpdater_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1065 DatabaseFilter -test -in DatabaseFilter_1.fasta -id DatabaseFilter_1.idXML -out DatabaseFilter_1_out.fasta.tmp > UTILS_DatabaseFilter_1.stdout 2> UTILS_DatabaseFilter_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1066 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DatabaseFilter_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DatabaseFilter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DatabaseFilter_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1067 DatabaseFilter -test -in DatabaseFilter_1.fasta -id DatabaseFilter_1.idXML -out DatabaseFilter_2_out.fasta.tmp -method blacklist > UTILS_DatabaseFilter_2.stdout 2> UTILS_DatabaseFilter_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1068 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DatabaseFilter_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DatabaseFilter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DatabaseFilter_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1069 DatabaseFilter -test -in DatabaseFilter_3.fasta -id DatabaseFilter_3.mzid -out DatabaseFilter_3_out.fasta.tmp > UTILS_DatabaseFilter_3.stdout 2> UTILS_DatabaseFilter_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1070 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DatabaseFilter_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DatabaseFilter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DatabaseFilter_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1071 DatabaseFilter -test -in DatabaseFilter_3.fasta -id DatabaseFilter_3.mzid -out DatabaseFilter_4_out.fasta.tmp -method blacklist > UTILS_DatabaseFilter_4.stdout 2> UTILS_DatabaseFilter_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1072 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DatabaseFilter_4 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DatabaseFilter_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DatabaseFilter_4.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1073 DecoyDatabase -test -in DecoyDatabase_1.fasta -out DecoyDatabase_1.fasta.tmp -only_decoy > UTILS_DecoyDatabase_1.stdout 2> UTILS_DecoyDatabase_1.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1074 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DecoyDatabase_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DecoyDatabase_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DecoyDatabase_1.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1075 DecoyDatabase -test -in DecoyDatabase_1.fasta -out DecoyDatabase_2.fasta.tmp -decoy_string "blabla" -decoy_string_position "prefix" -method shuffle -Decoy:non_shuffle_pattern "KRP" -seed 42 > UTILS_DecoyDatabase_2.stdout 2> UTILS_DecoyDatabase_2.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1076 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DecoyDatabase_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DecoyDatabase_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DecoyDatabase_2.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1077 DecoyDatabase -test -in DecoyDatabase_1.fasta -out DecoyDatabase_3.fasta.tmp -decoy_string "blabla" -decoy_string_position "prefix" -method shuffle -Decoy:non_shuffle_pattern "KR" -seed 42 -enzyme "Chymotrypsin" > UTILS_DecoyDatabase_3.stdout 2> UTILS_DecoyDatabase_3.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1078 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DecoyDatabase_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DecoyDatabase_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DecoyDatabase_3.stdout)";fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1079 DecoyDatabase -test -type RNA -in DecoyDatabase_4.fasta -out DecoyDatabase_4.fasta.tmp -decoy_string "blabla" -decoy_string_position "prefix" -method reverse -seed 42 > UTILS_DecoyDatabase_4.stdout 2> UTILS_DecoyDatabase_4.stderr
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
1080 if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DecoyDatabase_4 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DecoyDatabase_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DecoyDatabase_4.stdout)";fi