| Previous changeset 7:451ff602a957 (2016-04-25) Next changeset 9:5590b80e6e13 (2016-07-04) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82 |
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modified:
macros.xml planemo_test.sh tool_dependencies.xml |
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added:
test-data/Blanc04.mzXML |
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| diff -r 451ff602a957 -r 53923784176c macros.xml --- a/macros.xml Mon Apr 25 11:14:02 2016 -0400 +++ b/macros.xml Mon Jul 04 08:45:48 2016 -0400 |
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| @@ -3,9 +3,9 @@ <xml name="requirements"> <requirements> <requirement type="package" version="3.1.2">R</requirement> - <requirement type="package" version="0.4_1">r-snow</requirement> - <requirement type="package" version="1.44.0">bioconductor-xcms</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="0.4_1">r-snow</requirement> + <requirement type="package" version="1.46.0">bioconductor-xcms</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> </requirements> </xml> <xml name="stdio"> @@ -26,6 +26,30 @@ sh -c "exit \$return" </token> + <!-- zipfile load for planemo test --> + + <token name="@COMMAND_ZIPFILE_LOAD@"> + #if $zipfile_load_conditional.zip_file: + zipfile $zipfile_load_conditional.zip_file + #end if + </token> + + <xml name="zipfile_load"> + <conditional name="zipfile_load_conditional"> + <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." > + <option value="no" >no need</option> + <option value="yes" selected="peakgroups">yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> + </when> + </conditional> + </xml> + + + <token name="@HELP_AUTHORS@"> .. class:: infomark |
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| diff -r 451ff602a957 -r 53923784176c planemo_test.sh --- a/planemo_test.sh Mon Apr 25 11:14:02 2016 -0400 +++ b/planemo_test.sh Mon Jul 04 08:45:48 2016 -0400 |
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| @@ -1,13 +1,11 @@ # Example of planemo command to launch test -# Note: --galaxy_branch "dev" is set to deal with zip file - # -- Use of installed package environments # after having installing package on a local galaxy instance source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh -planemo test --install_galaxy --galaxy_branch "dev" +planemo test --install_galaxy #All 2 test(s) executed passed. #abims_xcms_xcmsSet[0]: passed @@ -17,7 +15,7 @@ # -- Use of conda dependencies planemo conda_init --conda_prefix /tmp/mc planemo conda_install --conda_prefix /tmp/mc . -planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution --galaxy_branch "dev" +planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution #All 2 test(s) executed passed. #abims_xcms_xcmsSet[0]: passed @@ -25,7 +23,7 @@ # -- Use of shed_test -planemo shed_test --install_galaxy -t testtoolshed --galaxy_branch ="dev" +planemo shed_test --install_galaxy -t testtoolshed #All 2 test(s) executed passed. #testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_xcmsset/2.0.8[0]: passed |
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| diff -r 451ff602a957 -r 53923784176c test-data/Blanc04.mzXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Blanc04.mzXML Mon Jul 04 08:45:48 2016 -0400 |
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| b'@@ -0,0 +1,40656 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2"\n+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\n+ xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd">\n+ <msRun scanCount="2031" startTime="PT0.7258S" endTime="PT1139.7S">\n+ <parentFile fileName="file://Y:/439020_Metabolomic database/Etienne/sacuri-rawToCentroid/Blanc04.RAW"\n+ fileType="RAWData"\n+ fileSha1="f556a3dff97784077240ef45afd63d28cf8d18d0"/>\n+ <msInstrument id="IC1">\n+ <msManufacturer category="msManufacturer" value="Thermo Scientific"/>\n+ <msModel category="msModel" value="LTQ Orbitrap Discovery"/>\n+ <msIonisation category="msIonisation" value="electrospray ionization"/>\n+ <msMassAnalyzer category="msMassAnalyzer" value="orbitrap"/>\n+ <msDetector category="msDetector" value="inductive detector"/>\n+ <software type="acquisition" name="Xcalibur" version="2.4 SP1"/>\n+ </msInstrument>\n+ <msInstrument id="IC2">\n+ <msManufacturer category="msManufacturer" value="Thermo Scientific"/>\n+ <msModel category="msModel" value="LTQ Orbitrap Discovery"/>\n+ <msIonisation category="msIonisation" value="electrospray ionization"/>\n+ <msMassAnalyzer category="msMassAnalyzer" value="radial ejection linear ion trap"/>\n+ <msDetector category="msDetector" value="electron multiplier"/>\n+ <software type="acquisition" name="Xcalibur" version="2.4 SP1"/>\n+ </msInstrument>\n+ <dataProcessing centroided="1">\n+ <software type="conversion" name="ProteoWizard" version="2.2.3214"/>\n+ <processingOperation name="Conversion to mzML"/>\n+ <software type="processing" name="ProteoWizard" version="2.2.3214"/>\n+ <comment>Thermo/Xcalibur peak picking</comment>\n+ </dataProcessing>\n+ <scan num="1"\n+ scanEvent="1"\n+ scanType="FULL"\n+ centroided="1"\n+ msLevel="1"\n+ peaksCount="319"\n+ polarity="-"\n+ retentionTime="PT0.7258S"\n+ lowMz="50.045391082764"\n+ highMz="988.520263671875"\n+ basePeakMz="91.003479003906"\n+ basePeakIntensity="4.8688715e06"\n+ totIonCurrent="8.552763e06"\n+ msInstrumentID="IC1">\n+ <peaks compressedLen="0"\n+ precision="32"\n+ byteOrder="network"\n+ pairOrder="m/z-int">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'..b'>\n+ 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| diff -r 451ff602a957 -r 53923784176c tool_dependencies.xml --- a/tool_dependencies.xml Mon Apr 25 11:14:02 2016 -0400 +++ b/tool_dependencies.xml Mon Jul 04 08:45:48 2016 -0400 |
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| @@ -3,7 +3,7 @@ <package name="R" version="3.1.2"> <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="bioconductor-xcms" version="1.44.0"> - <repository changeset_revision="58ebb405a3d6" name="package_bioconductor_xcms_1_44_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="bioconductor-xcms" version="1.46.0"> + <repository changeset_revision="779207ed5674" name="package_bioconductor_xcms_1_46_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |