# HG changeset patch # User galaxyp # Date 1502284977 14400 # Node ID 36da1e3613ea600f2fa008018a4b52bbde8b721d # Parent ec7b8772f4c9aeb973b84199c03035d8ddff5204 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 diff -r ec7b8772f4c9 -r 36da1e3613ea MascotAdapter.xml --- a/MascotAdapter.xml Wed Mar 01 12:35:50 2017 -0500 +++ b/MascotAdapter.xml Wed Aug 09 09:22:57 2017 -0400 @@ -1,7 +1,7 @@ - + Annotates MS/MS spectra using Mascot. MascotAdapter @@ -34,7 +34,12 @@ -peak_mass_tolerance $param_peak_mass_tolerance #end if #if $param_taxonomy: - -taxonomy $param_taxonomy + -taxonomy + #if " " in str($param_taxonomy): + "$param_taxonomy" + #else + $param_taxonomy + #end if #end if #if $rep_param_modifications: @@ -76,7 +81,12 @@ -hits "$param_hits" #end if #if $param_cleavage: - -cleavage $param_cleavage + -cleavage + #if " " in str($param_cleavage): + "$param_cleavage" + #else + $param_cleavage + #end if #end if #if $param_missed_cleavages: -missed_cleavages $param_missed_cleavages @@ -112,7 +122,12 @@ -boundary "$param_boundary" #end if #if $param_mass_type: - -mass_type $param_mass_type + -mass_type + #if " " in str($param_mass_type): + "$param_mass_type" + #else + $param_mass_type + #end if #end if #if $param_mascot_directory: -mascot_directory "$param_mascot_directory" @@ -127,7 +142,7 @@ #end if - + diff -r ec7b8772f4c9 -r 36da1e3613ea datatypes_conf.xml --- a/datatypes_conf.xml Wed Mar 01 12:35:50 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r ec7b8772f4c9 -r 36da1e3613ea filetypes.txt --- a/filetypes.txt Wed Mar 01 12:35:50 2017 -0500 +++ b/filetypes.txt Wed Aug 09 09:22:57 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 ec7b8772f4c9 -r 36da1e3613ea macros.xml --- a/macros.xml Wed Mar 01 12:35:50 2017 -0500 +++ b/macros.xml Wed Aug 09 09:22:57 2017 -0400 @@ -2,7 +2,7 @@ - openms + openms xtandem fido msgf_plus diff -r ec7b8772f4c9 -r 36da1e3613ea readme.md --- a/readme.md Wed Mar 01 12:35:50 2017 -0500 +++ b/readme.md Wed Aug 09 09:22:57 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 ec7b8772f4c9 -r 36da1e3613ea tool.conf --- a/tool.conf Wed Mar 01 12:35:50 2017 -0500 +++ b/tool.conf Wed Aug 09 09:22:57 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 @@ - -