# HG changeset patch # User galaxyp # Date 1502285269 14400 # Node ID 289009115eb2887c52982615ee8a48527f2c7c4d # Parent 2c8729a286ea5c575a683c6901a2366af229525c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 diff -r 2c8729a286ea -r 289009115eb2 MRMTransitionGroupPicker.xml --- a/MRMTransitionGroupPicker.xml Wed Mar 01 12:38:23 2017 -0500 +++ b/MRMTransitionGroupPicker.xml Wed Aug 09 09:27:49 2017 -0400 @@ -1,7 +1,8 @@ - + + Picks peaks in SRM/MRM chromatograms. MRMTransitionGroupPicker macros.xml @@ -36,7 +37,12 @@ -algorithm:PeakPickerMRM:gauss_width $param_algorithm_PeakPickerMRM_gauss_width #end if #if $param_algorithm_PeakPickerMRM_use_gauss: - -algorithm:PeakPickerMRM:use_gauss $param_algorithm_PeakPickerMRM_use_gauss + -algorithm:PeakPickerMRM:use_gauss + #if " " in str($param_algorithm_PeakPickerMRM_use_gauss): + "$param_algorithm_PeakPickerMRM_use_gauss" + #else + $param_algorithm_PeakPickerMRM_use_gauss + #end if #end if #if $param_algorithm_PeakPickerMRM_peak_width: -algorithm:PeakPickerMRM:peak_width $param_algorithm_PeakPickerMRM_peak_width @@ -51,13 +57,23 @@ -algorithm:PeakPickerMRM:sn_bin_count $param_algorithm_PeakPickerMRM_sn_bin_count #end if #if $param_algorithm_PeakPickerMRM_write_sn_log_messages: - -algorithm:PeakPickerMRM:write_sn_log_messages $param_algorithm_PeakPickerMRM_write_sn_log_messages + -algorithm:PeakPickerMRM:write_sn_log_messages + #if " " in str($param_algorithm_PeakPickerMRM_write_sn_log_messages): + "$param_algorithm_PeakPickerMRM_write_sn_log_messages" + #else + $param_algorithm_PeakPickerMRM_write_sn_log_messages + #end if #end if #if $param_algorithm_PeakPickerMRM_remove_overlapping_peaks: -algorithm:PeakPickerMRM:remove_overlapping_peaks #end if #if $param_algorithm_PeakPickerMRM_method: - -algorithm:PeakPickerMRM:method $param_algorithm_PeakPickerMRM_method + -algorithm:PeakPickerMRM:method + #if " " in str($param_algorithm_PeakPickerMRM_method): + "$param_algorithm_PeakPickerMRM_method" + #else + $param_algorithm_PeakPickerMRM_method + #end if #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: @@ -67,10 +83,18 @@ -algorithm:min_peak_width $adv_opts.param_algorithm_min_peak_width #end if #if $adv_opts.param_algorithm_background_subtraction: - -algorithm:background_subtraction $adv_opts.param_algorithm_background_subtraction + -algorithm:background_subtraction + #if " " in str($adv_opts.param_algorithm_background_subtraction): + "$adv_opts.param_algorithm_background_subtraction" + #else + $adv_opts.param_algorithm_background_subtraction + #end if #end if #if $adv_opts.param_algorithm_recalculate_peaks: - -algorithm:recalculate_peaks "$adv_opts.param_algorithm_recalculate_peaks" + -algorithm:recalculate_peaks +#end if + #if $adv_opts.param_algorithm_use_precursors: + -algorithm:use_precursors #end if #if $adv_opts.param_algorithm_recalculate_peaks_max_z: -algorithm:recalculate_peaks_max_z $adv_opts.param_algorithm_recalculate_peaks_max_z @@ -79,7 +103,7 @@ -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality #end if #if $adv_opts.param_algorithm_compute_peak_quality: - -algorithm:compute_peak_quality "$adv_opts.param_algorithm_compute_peak_quality" + -algorithm:compute_peak_quality #end if #end if @@ -117,31 +141,18 @@ - - - - - - - - + + - - - - - - - - + - None + Picks peaks in SRM/MRM chromatograms. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_MRMTransitionGroupPicker.html +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMTransitionGroupPicker.html diff -r 2c8729a286ea -r 289009115eb2 datatypes_conf.xml --- a/datatypes_conf.xml Wed Mar 01 12:38:23 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2c8729a286ea -r 289009115eb2 filetypes.txt --- a/filetypes.txt Wed Mar 01 12:38:23 2017 -0500 +++ b/filetypes.txt Wed Aug 09 09:27:49 2017 -0400 @@ -14,7 +14,7 @@ consensusXML consensusxml galaxy.datatypes.proteomics:ConsensusXML application/xml edta tabular galaxy.datatypes.tabular:Tabular featureXML featurexml galaxy.datatypes.proteomics:FeatureXML application/xml -idXML idxml galaxy.datatypes.proteomics:IdXM application/xml +idXML idxml galaxy.datatypes.proteomics:IdXML application/xml mzML mzml galaxy.datatypes.proteomics:MzML application/xml mzXML mzxml galaxy.datatypes.proteomics:MzXML application/xml pepXML pepxml galaxy.datatypes.proteomics:PepXml application/xml @@ -26,4 +26,4 @@ msp msp galaxy.datatypes.proteomics:Msp mzid mzid galaxy.datatypes.proteomics:MzIdentML application/xml png png galaxy.datatypes.images:Png image/png -mgf mgf galaxy.datatypes.proteomics:Mgf \ No newline at end of file +mgf mgf galaxy.datatypes.proteomics:Mgf diff -r 2c8729a286ea -r 289009115eb2 macros.xml --- a/macros.xml Wed Mar 01 12:38:23 2017 -0500 +++ b/macros.xml Wed Aug 09 09:27:49 2017 -0400 @@ -2,7 +2,7 @@ - openms + openms xtandem fido msgf_plus diff -r 2c8729a286ea -r 289009115eb2 readme.md --- a/readme.md Wed Mar 01 12:38:23 2017 -0500 +++ b/readme.md Wed Aug 09 09:27:49 2017 -0400 @@ -14,15 +14,29 @@ Generating OpenMS wrappers ========================== - * install OpenMS (you can do this automatically through the Tool Shed) + * install OpenMS (you can do this automatically through Conda) * create a folder called CTD - * inside of your new installed openms/bin folder, execute the following command: + * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory: ```bash for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; ``` - * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`). + * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow: + + ```bash + ls >> tools.txt + ``` + + * search for the `bin` folder of your conda environment containing OpenMS and do: + + ```bash + while read p; do + ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD; + done ``` - * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line + + * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): - -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit - - and change it to + ``` + + ``` + + * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.: - + - `` + - `` * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files. diff -r 2c8729a286ea -r 289009115eb2 tool.conf --- a/tool.conf Wed Mar 01 12:38:23 2017 -0500 +++ b/tool.conf Wed Aug 09 09:27:49 2017 -0400 @@ -6,13 +6,7 @@ -
- - -
- - @@ -22,13 +16,17 @@ + + +
+ @@ -44,7 +42,6 @@ - @@ -62,12 +59,14 @@ + + @@ -78,6 +77,7 @@ +
@@ -154,9 +154,7 @@ - -