| Previous changeset 4:4d26f6100cae (2018-01-11) Next changeset 6:f01f84cbd265 (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:
OpenSwathRTNormalizer.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 4d26f6100cae -r d55a7181895c OpenSwathRTNormalizer.xml --- a/OpenSwathRTNormalizer.xml Thu Jan 11 17:36:26 2018 -0500 +++ b/OpenSwathRTNormalizer.xml Mon Feb 12 12:55:30 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: [Targeted Experiments]-->\n-<tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.2.0">\n+<tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.3.0">\n <description>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.</description>\n <macros>\n <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token>\n@@ -34,6 +34,26 @@\n #if $param_estimateBestPeptides:\n -estimateBestPeptides\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_algorithm_stop_report_after_feature:\n -algorithm:stop_report_after_feature $param_algorithm_stop_report_after_feature\n #end if\n@@ -124,26 +144,6 @@\n #if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff:\n -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff\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_peptideEstimation_InitialQualityCutoff:\n -peptideEstimation:InitialQualityCutoff $param_peptideEstimation_InitialQualityCutoff\n #end if\n@@ -198,6 +198,9 @@\n #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality:\n -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality\n #end if\n+ #if $adv_opts.param_algorithm_TransitionGroupPicker_resample_boundary:\n+ -algorithm:TransitionGroupPicker:resample_boundary $adv_opts.param_algorithm_TransitionGroupPicker_resample_boundary\n+#end if\n #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:\n -algorithm:TransitionGroupPicker:compute_peak_quality\n #end if\n@@ -324,6 +327,16 @@\n <param name="param_min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help="(-min_rsq) "/>\n <param name="param_min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help="(-min_coverage) "/>\n <param name="param_estimateBestPeptides" display='..b'iveChauvenet" display="radio" type="boolean" truevalue="-outlierDetection:useIterativeChauvenet" falsevalue="" checked="false" optional="True" label="Whether to use Chauvenet\'s criterion when using iterative methods" help="(-useIterativeChauvenet) This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained"/>\n- <param name="param_outlierDetection_RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help="(-RANSACMaxIterations) "/>\n- <param name="param_outlierDetection_RANSACMaxPercentRTThreshold" type="integer" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="(-RANSACMaxPercentRTThreshold) 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_peptideEstimation_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_peptideEstimation_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_peptideEstimation_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@@ -390,6 +393,7 @@\n <param name="param_algorithm_TransitionGroupPicker_use_precursors" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>\n <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>\n <param name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>\n+ <param name="param_algorithm_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_algorithm_TransitionGroupPicker_compute_peak_quality" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:compute_peak_quality" falsevalue="" checked="false" optional="True" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>\n <param name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help="(-interpolation_step) "/>\n <param name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help="(-tolerance_stdev_bounding_box) "/>\n' |
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| diff -r 4d26f6100cae -r d55a7181895c SKIP_TOOLS_FILE.txt --- a/SKIP_TOOLS_FILE.txt Thu Jan 11 17:36:26 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 4d26f6100cae -r d55a7181895c macros.xml --- a/macros.xml Thu Jan 11 17:36:26 2018 -0500 +++ b/macros.xml Mon Feb 12 12:55:30 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 4d26f6100cae -r d55a7181895c readme.md --- a/readme.md Thu Jan 11 17:36:26 2018 -0500 +++ b/readme.md Mon Feb 12 12:55:30 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 4d26f6100cae -r d55a7181895c tools_blacklist.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools_blacklist.txt Mon Feb 12 12:55:30 2018 -0500 |
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| @@ -0,0 +1,9 @@ +OMSSAAdapter +MyriMatchAdapter +PepNovoAdapter +SeedListGenerator +SpecLibSearcher +MapAlignerIdentification +MapAlignerPoseClustering +MapAlignerSpectrum +MapAlignerRTTransformer |