# HG changeset patch # User galaxyp # Date 1502285469 14400 # Node ID 68f1d9c0c6ca484a3140e97df8ba4675e4c14178 # Parent a337220a26a067ad2e9a8b04ccabdccf37ad2a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 diff -r a337220a26a0 -r 68f1d9c0c6ca LuciphorAdapter.xml --- a/LuciphorAdapter.xml Wed Mar 01 12:40:51 2017 -0500 +++ b/LuciphorAdapter.xml Wed Aug 09 09:31:09 2017 -0400 @@ -1,7 +1,7 @@ - + Modification site localisation using LuciPHOr2. LuciphorAdapter @@ -22,13 +22,23 @@ -out $param_out #end if #if $param_fragment_method: - -fragment_method $param_fragment_method + -fragment_method + #if " " in str($param_fragment_method): + "$param_fragment_method" + #else + $param_fragment_method + #end if #end if #if $param_fragment_mass_tolerance: -fragment_mass_tolerance $param_fragment_mass_tolerance #end if #if $param_fragment_error_units: - -fragment_error_units $param_fragment_error_units + -fragment_error_units + #if " " in str($param_fragment_error_units): + "$param_fragment_error_units" + #else + $param_fragment_error_units + #end if #end if #if $param_min_mz: -min_mz $param_min_mz @@ -91,7 +101,12 @@ -num_threads $param_num_threads #end if #if $param_run_mode: - -run_mode $param_run_mode + -run_mode + #if " " in str($param_run_mode): + "$param_run_mode" + #else + $param_run_mode + #end if #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: @@ -114,6 +129,7 @@ + @@ -136,6 +152,7 @@ + @@ -267,7 +284,6 @@ - @@ -292,23 +308,28 @@ + + + - + - - + + + + @@ -329,6 +350,226 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -340,6 +581,7 @@ + @@ -357,9 +599,11 @@ + + @@ -373,6 +617,7 @@ + @@ -394,6 +639,7 @@ + @@ -425,6 +671,7 @@ + @@ -435,6 +682,8 @@ + + @@ -527,7 +776,7 @@ - + @@ -537,6 +786,7 @@ + @@ -600,10 +850,16 @@ + + + + + + @@ -619,6 +875,7 @@ + @@ -686,6 +943,7 @@ + @@ -696,6 +954,7 @@ + @@ -710,6 +969,7 @@ + @@ -750,13 +1010,16 @@ + + + + - - + @@ -826,48 +1089,353 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -896,6 +1464,7 @@ + @@ -950,8 +1519,11 @@ + + + @@ -981,7 +1553,6 @@ - @@ -1105,13 +1676,29 @@ - + + + + + + + + + + + + + + + + + @@ -1128,6 +1715,7 @@ + @@ -1159,6 +1747,8 @@ + + @@ -1208,6 +1798,7 @@ + @@ -1227,6 +1818,8 @@ + + @@ -1258,6 +1851,10 @@ + + + + @@ -1321,6 +1918,9 @@ + + + @@ -1342,6 +1942,8 @@ + + @@ -1363,9 +1965,6 @@ - - - @@ -1434,7 +2033,7 @@ - + @@ -1472,6 +2071,9 @@ + + + @@ -1493,6 +2095,8 @@ + + @@ -1584,6 +2188,7 @@ + @@ -1596,6 +2201,8 @@ + + @@ -1613,21 +2220,358 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -1707,6 +2651,10 @@ + + + + diff -r a337220a26a0 -r 68f1d9c0c6ca datatypes_conf.xml --- a/datatypes_conf.xml Wed Mar 01 12:40:51 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r a337220a26a0 -r 68f1d9c0c6ca filetypes.txt --- a/filetypes.txt Wed Mar 01 12:40:51 2017 -0500 +++ b/filetypes.txt Wed Aug 09 09:31:09 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 a337220a26a0 -r 68f1d9c0c6ca macros.xml --- a/macros.xml Wed Mar 01 12:40:51 2017 -0500 +++ b/macros.xml Wed Aug 09 09:31:09 2017 -0400 @@ -2,7 +2,7 @@ - openms + openms xtandem fido msgf_plus diff -r a337220a26a0 -r 68f1d9c0c6ca readme.md --- a/readme.md Wed Mar 01 12:40:51 2017 -0500 +++ b/readme.md Wed Aug 09 09:31:09 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 a337220a26a0 -r 68f1d9c0c6ca tool.conf --- a/tool.conf Wed Mar 01 12:40:51 2017 -0500 +++ b/tool.conf Wed Aug 09 09:31:09 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 @@ - -