| Previous changeset 4:1734e2933b2b (2018-01-11) Next changeset 6:94d245e69164 (2018-03-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b |
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modified:
OpenSwathWorkflow.xml macros.xml readme.md |
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added:
tools_blacklist.txt |
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removed:
SKIP_TOOLS_FILE.txt |
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| diff -r 1734e2933b2b -r 56988709dec6 OpenSwathWorkflow.xml --- a/OpenSwathWorkflow.xml Thu Jan 11 18:12:54 2018 -0500 +++ b/OpenSwathWorkflow.xml Mon Feb 12 13:02:55 2018 -0500 |
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| b'@@ -1,7 +1,7 @@\n <?xml version=\'1.0\' encoding=\'UTF-8\'?>\n-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->\n+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->\n <!--Proposed Tool Section: [Utilities]-->\n-<tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.2.0.1">\n+<tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.3.0">\n <description>Complete workflow to run OpenSWATH</description>\n <macros>\n <token name="@EXECUTABLE@">OpenSwathWorkflow</token>\n@@ -54,6 +54,58 @@\n #if $param_sonar:\n -sonar\n #end if\n+#if $param_RTNormalization_alignmentMethod:\n+ -RTNormalization:alignmentMethod\n+ #if " " in str($param_RTNormalization_alignmentMethod):\n+ "$param_RTNormalization_alignmentMethod"\n+ #else\n+ $param_RTNormalization_alignmentMethod\n+ #end if\n+#end if\n+#if $param_RTNormalization_outlierMethod:\n+ -RTNormalization:outlierMethod\n+ #if " " in str($param_RTNormalization_outlierMethod):\n+ "$param_RTNormalization_outlierMethod"\n+ #else\n+ $param_RTNormalization_outlierMethod\n+ #end if\n+#end if\n+#if $param_RTNormalization_useIterativeChauvenet:\n+ -RTNormalization:useIterativeChauvenet\n+#end if\n+#if $param_RTNormalization_RANSACMaxIterations:\n+ -RTNormalization:RANSACMaxIterations $param_RTNormalization_RANSACMaxIterations\n+#end if\n+#if $param_RTNormalization_RANSACMaxPercentRTThreshold:\n+ -RTNormalization:RANSACMaxPercentRTThreshold $param_RTNormalization_RANSACMaxPercentRTThreshold\n+#end if\n+#if $param_RTNormalization_RANSACSamplingSize:\n+ -RTNormalization:RANSACSamplingSize $param_RTNormalization_RANSACSamplingSize\n+#end if\n+#if $param_RTNormalization_estimateBestPeptides:\n+ -RTNormalization:estimateBestPeptides\n+#end if\n+#if $param_RTNormalization_InitialQualityCutoff:\n+ -RTNormalization:InitialQualityCutoff $param_RTNormalization_InitialQualityCutoff\n+#end if\n+#if $param_RTNormalization_OverallQualityCutoff:\n+ -RTNormalization:OverallQualityCutoff $param_RTNormalization_OverallQualityCutoff\n+#end if\n+#if $param_RTNormalization_NrRTBins:\n+ -RTNormalization:NrRTBins $param_RTNormalization_NrRTBins\n+#end if\n+#if $param_RTNormalization_MinPeptidesPerBin:\n+ -RTNormalization:MinPeptidesPerBin $param_RTNormalization_MinPeptidesPerBin\n+#end if\n+#if $param_RTNormalization_MinBinsFilled:\n+ -RTNormalization:MinBinsFilled $param_RTNormalization_MinBinsFilled\n+#end if\n+#if $param_RTNormalization_lowess_span:\n+ -RTNormalization:lowess:span $param_RTNormalization_lowess_span\n+#end if\n+#if $param_RTNormalization_b_spline_num_nodes:\n+ -RTNormalization:b_spline:num_nodes $param_RTNormalization_b_spline_num_nodes\n+#end if\n #if $param_Scoring_stop_report_after_feature:\n -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature\n #end if\n@@ -163,44 +215,6 @@\n #if $param_Scoring_EMGScoring_max_iteration:\n -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration\n #end if\n-#if $param_outlierDetection_outlierMethod:\n- -outlierDetection:outlierMethod\n- #if " " in str($param_outlierDetection_outlierMethod):\n- "$param_outlierDetection_outlierMethod"\n- #else\n- $param_outlierDetection_outlierMethod\n- #end if\n-#end if\n-#if $param_outlierDetection_useIterativeChauvenet:\n- -outlierDetection:useIterativeChauvenet\n-#end if\n-#if $param_outlierDetection_RANSACMaxIterations:\n- -outlierDetection:RANSACMaxIterations $param_outlierDetection_RANSACMaxIterations\n-#end if\n-#if $param_outlierDetection_RANSACMaxPercentRTThreshold:\n- -outlierDetection:RANSACMaxPercentRTThreshold $param_outlierDetection_RANSACMaxPercentRTThreshold\n-#end if\n-#if $param_outlierDetection_RANSACSamplingSize:\n- -outlierDetection:RANSACSamplingSize $param_outlierDetection_RANSACSamplingSize\n-#end if\n-#if $param_outlierDetection_estimateBestPeptides:\n- -outlierDete'..b'tRTThreshold) Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/>\n- <param name="param_outlierDetection_RANSACSamplingSize" type="integer" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help="(-RANSACSamplingSize) "/>\n- <param name="param_outlierDetection_estimateBestPeptides" display="radio" type="boolean" truevalue="-outlierDetection:estimateBestPeptides" falsevalue="" checked="false" optional="True" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization. Use this option you do not expect all your peptides to be detected in a sample and too many \'bad\' peptides enter the outlier removal step (" help="(-estimateBestPeptides) e.g. due to them being endogenous peptides or using a less curated list of peptides)"/>\n- <param name="param_outlierDetection_InitialQualityCutoff" type="float" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="(-InitialQualityCutoff) -2 to 2)"/>\n- <param name="param_outlierDetection_OverallQualityCutoff" type="float" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="(-OverallQualityCutoff) 0 to 10)"/>\n- <param name="param_outlierDetection_NrRTBins" type="integer" value="10" label="Number of RT bins to use to compute coverage" help="(-NrRTBins) This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/>\n- <param name="param_outlierDetection_MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as \'covered\'" help="(-MinPeptidesPerBin) "/>\n- <param name="param_outlierDetection_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled) "/>\n <expand macro="advanced_options">\n <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) If set, tr_irt may be omitted"/>\n <param name="param_swath_windows_file" type="data" format="txt" label="Optional, tab separated file containing the SWATH windows for extraction: lower_offset upper_offset \\newline 400 425 \\newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>\n@@ -517,6 +542,7 @@\n <param name="param_Scoring_quantification_cutoff" type="float" min="0.0" optional="True" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help="(-quantification_cutoff) "/>\n <param name="param_Scoring_write_convex_hull" display="radio" type="boolean" truevalue="-Scoring:write_convex_hull" falsevalue="" checked="false" optional="True" label="Whether to write out all points of all features into the featureXML" help="(-write_convex_hull) "/>\n <param name="param_Scoring_TransitionGroupPicker_use_precursors" display="radio" type="boolean" truevalue="-Scoring:TransitionGroupPicker:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>\n+ <param name="param_Scoring_TransitionGroupPicker_resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help="(-resample_boundary) "/>\n <param name="param_Scoring_Scores_use_shape_score" display="radio" type="select" optional="False" value="true" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help="(-use_shape_score) ">\n <option value="true" selected="true">true</option>\n <option value="false">false</option>\n' |
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| diff -r 1734e2933b2b -r 56988709dec6 SKIP_TOOLS_FILE.txt --- a/SKIP_TOOLS_FILE.txt Thu Jan 11 18:12:54 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -OMSSAAdapter -MyriMatchAdapter -PepNovoAdapter -SeedListGenerator -SpecLibSearcher -MapAlignerIdentification -MapAlignerPoseClustering -MapAlignerSpectrum -MapAlignerRTTransformer |
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| diff -r 1734e2933b2b -r 56988709dec6 macros.xml --- a/macros.xml Thu Jan 11 18:12:54 2018 -0500 +++ b/macros.xml Mon Feb 12 13:02:55 2018 -0500 |
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| @@ -2,10 +2,10 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.2">openms</requirement> + <requirement type="package" version="2.3">openms</requirement> <requirement type="package" version="15.12.15.2">xtandem</requirement> <requirement type="package" version="1.0">fido</requirement> - <requirement type="package" version="2016.10.26">msgf_plus</requirement> + <requirement type="package" version="2017.07.21">msgf_plus</requirement> <yield/> </requirements> </xml> |
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| diff -r 1734e2933b2b -r 56988709dec6 readme.md --- a/readme.md Thu Jan 11 18:12:54 2018 -0500 +++ b/readme.md Mon Feb 12 13:02:55 2018 -0500 |
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| @@ -53,29 +53,29 @@ * clone or install CTD2Galaxy ```bash - git clone https://github.com/WorkflowConversion/CTD2Galaxy.git + git clone https://github.com/WorkflowConversion/CTDConverter.git ``` - * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it. + * If you have CTDopts and CTDConverter installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it. Further information can be found on the CTDConverter page. ```bash - python generator.py \ + python convert.py galaxy \ -i /PATH/TO/YOUR/CTD/*.ctd \ -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ -d datatypes_conf.xml -g openms \ -b version log debug test no_progress threads \ in_type executable myrimatch_executable \ fido_executable fidocp_executable \ - omssa_executable pepnovo_executable \ + omssa_executable pepnovo_e xecutable \ xtandem_executable param_model_directory \ java_executable java_memory java_permgen \ r_executable rt_concat_trafo_out param_id_pool \ -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ - -s PATH/TO/SKIP_TOOLS_FILES.txt + -s PATH/TO/tools_blacklist.txt ``` - * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: + * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. Some of these tools might already be deprecated and the files might not exist: ``` sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml @@ -171,8 +171,8 @@ ``` - * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in - by the automatic conversion step and are therefore in `SKIP_TOOLS_FILES.txt`: + * `This section might not be up to date. It might be worth trying if these tools will run now.` These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in + by the automatic conversion step and are therefore in `tools_blacklist.txt`: * SeedListGenerator * SpecLibSearcher * MapAlignerIdentification |
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| diff -r 1734e2933b2b -r 56988709dec6 tools_blacklist.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools_blacklist.txt Mon Feb 12 13:02:55 2018 -0500 |
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| @@ -0,0 +1,9 @@ +OMSSAAdapter +MyriMatchAdapter +PepNovoAdapter +SeedListGenerator +SpecLibSearcher +MapAlignerIdentification +MapAlignerPoseClustering +MapAlignerSpectrum +MapAlignerRTTransformer |