Mercurial > repos > galaxyp > openms_mssimulator
changeset 1:0d788b696572 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:41:04 -0400 (2017-04-18) |
| parents | ae8e96c8f9a4 |
| children | b8103b8deae2 |
| files | MSSimulator.xml readme.md |
| diffstat | 2 files changed, 98 insertions(+), 25 deletions(-) [+] |
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--- a/MSSimulator.xml Wed Mar 01 10:21:04 2017 -0500 +++ b/MSSimulator.xml Tue Apr 18 15:41:04 2017 -0400 @@ -38,10 +38,20 @@ -out_id $param_out_id #end if #if $param_algorithm_MSSim_Digestion_enzyme: - -algorithm:MSSim:Digestion:enzyme $param_algorithm_MSSim_Digestion_enzyme + -algorithm:MSSim:Digestion:enzyme + #if " " in str($param_algorithm_MSSim_Digestion_enzyme): + "$param_algorithm_MSSim_Digestion_enzyme" + #else + $param_algorithm_MSSim_Digestion_enzyme + #end if #end if #if $param_algorithm_MSSim_Digestion_model: - -algorithm:MSSim:Digestion:model $param_algorithm_MSSim_Digestion_model + -algorithm:MSSim:Digestion:model + #if " " in str($param_algorithm_MSSim_Digestion_model): + "$param_algorithm_MSSim_Digestion_model" + #else + $param_algorithm_MSSim_Digestion_model + #end if #end if #if $param_algorithm_MSSim_Digestion_min_peptide_length: -algorithm:MSSim:Digestion:min_peptide_length $param_algorithm_MSSim_Digestion_min_peptide_length @@ -53,10 +63,20 @@ -algorithm:MSSim:Digestion:model_naive:missed_cleavages $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages #end if #if $param_algorithm_MSSim_RT_rt_column: - -algorithm:MSSim:RT:rt_column $param_algorithm_MSSim_RT_rt_column + -algorithm:MSSim:RT:rt_column + #if " " in str($param_algorithm_MSSim_RT_rt_column): + "$param_algorithm_MSSim_RT_rt_column" + #else + $param_algorithm_MSSim_RT_rt_column + #end if #end if #if $param_algorithm_MSSim_RT_auto_scale: - -algorithm:MSSim:RT:auto_scale $param_algorithm_MSSim_RT_auto_scale + -algorithm:MSSim:RT:auto_scale + #if " " in str($param_algorithm_MSSim_RT_auto_scale): + "$param_algorithm_MSSim_RT_auto_scale" + #else + $param_algorithm_MSSim_RT_auto_scale + #end if #end if #if $param_algorithm_MSSim_RT_total_gradient_time: -algorithm:MSSim:RT:total_gradient_time $param_algorithm_MSSim_RT_total_gradient_time @@ -167,16 +187,31 @@ -algorithm:MSSim:Ionization:mz:upper_measurement_limit $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit #end if #if $param_algorithm_MSSim_RawSignal_enabled: - -algorithm:MSSim:RawSignal:enabled $param_algorithm_MSSim_RawSignal_enabled + -algorithm:MSSim:RawSignal:enabled + #if " " in str($param_algorithm_MSSim_RawSignal_enabled): + "$param_algorithm_MSSim_RawSignal_enabled" + #else + $param_algorithm_MSSim_RawSignal_enabled + #end if #end if #if $param_algorithm_MSSim_RawSignal_peak_shape: - -algorithm:MSSim:RawSignal:peak_shape $param_algorithm_MSSim_RawSignal_peak_shape + -algorithm:MSSim:RawSignal:peak_shape + #if " " in str($param_algorithm_MSSim_RawSignal_peak_shape): + "$param_algorithm_MSSim_RawSignal_peak_shape" + #else + $param_algorithm_MSSim_RawSignal_peak_shape + #end if #end if #if $param_algorithm_MSSim_RawSignal_resolution_value: -algorithm:MSSim:RawSignal:resolution:value $param_algorithm_MSSim_RawSignal_resolution_value #end if #if $param_algorithm_MSSim_RawSignal_resolution_type: - -algorithm:MSSim:RawSignal:resolution:type $param_algorithm_MSSim_RawSignal_resolution_type + -algorithm:MSSim:RawSignal:resolution:type + #if " " in str($param_algorithm_MSSim_RawSignal_resolution_type): + "$param_algorithm_MSSim_RawSignal_resolution_type" + #else + $param_algorithm_MSSim_RawSignal_resolution_type + #end if #end if #if $param_algorithm_MSSim_RawSignal_baseline_scaling: -algorithm:MSSim:RawSignal:baseline:scaling $param_algorithm_MSSim_RawSignal_baseline_scaling @@ -221,7 +256,12 @@ -algorithm:MSSim:RawSignal:noise:detector:stddev $param_algorithm_MSSim_RawSignal_noise_detector_stddev #end if #if $param_algorithm_MSSim_RawTandemSignal_status: - -algorithm:MSSim:RawTandemSignal:status $param_algorithm_MSSim_RawTandemSignal_status + -algorithm:MSSim:RawTandemSignal:status + #if " " in str($param_algorithm_MSSim_RawTandemSignal_status): + "$param_algorithm_MSSim_RawTandemSignal_status" + #else + $param_algorithm_MSSim_RawTandemSignal_status + #end if #end if #if $param_algorithm_MSSim_RawTandemSignal_tandem_mode: -algorithm:MSSim:RawTandemSignal:tandem_mode $param_algorithm_MSSim_RawTandemSignal_tandem_mode @@ -319,10 +359,20 @@ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion #end if #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions: - -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions + #if " " in str($param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions): + "$param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions" + #else + $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions + #end if #end if #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions: - -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions + #if " " in str($param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions): + "$param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions" + #else + $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions + #end if #end if #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions: -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions @@ -427,16 +477,31 @@ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity #end if #if $param_algorithm_MSSim_Global_ionization_type: - -algorithm:MSSim:Global:ionization_type $param_algorithm_MSSim_Global_ionization_type + -algorithm:MSSim:Global:ionization_type + #if " " in str($param_algorithm_MSSim_Global_ionization_type): + "$param_algorithm_MSSim_Global_ionization_type" + #else + $param_algorithm_MSSim_Global_ionization_type + #end if #end if #if $param_algorithm_MSSim_Labeling_type: - -algorithm:MSSim:Labeling:type $param_algorithm_MSSim_Labeling_type + -algorithm:MSSim:Labeling:type + #if " " in str($param_algorithm_MSSim_Labeling_type): + "$param_algorithm_MSSim_Labeling_type" + #else + $param_algorithm_MSSim_Labeling_type + #end if #end if #if $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift: -algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift #end if #if $param_algorithm_MSSim_Labeling_ICPL_label_proteins: - -algorithm:MSSim:Labeling:ICPL:label_proteins $param_algorithm_MSSim_Labeling_ICPL_label_proteins + -algorithm:MSSim:Labeling:ICPL:label_proteins + #if " " in str($param_algorithm_MSSim_Labeling_ICPL_label_proteins): + "$param_algorithm_MSSim_Labeling_ICPL_label_proteins" + #else + $param_algorithm_MSSim_Labeling_ICPL_label_proteins + #end if #end if #if $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift: -algorithm:MSSim:Labeling:SILAC:fixed_rtshift $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift @@ -454,7 +519,12 @@ -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine" #end if #if $param_algorithm_MSSim_Labeling_itraq_iTRAQ: - -algorithm:MSSim:Labeling:itraq:iTRAQ $param_algorithm_MSSim_Labeling_itraq_iTRAQ + -algorithm:MSSim:Labeling:itraq:iTRAQ + #if " " in str($param_algorithm_MSSim_Labeling_itraq_iTRAQ): + "$param_algorithm_MSSim_Labeling_itraq_iTRAQ" + #else + $param_algorithm_MSSim_Labeling_itraq_iTRAQ + #end if #end if #if $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift: -algorithm:MSSim:Labeling:itraq:reporter_mass_shift $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift @@ -488,10 +558,20 @@ -algorithm:MSSim:Labeling:o18:labeling_efficiency $param_algorithm_MSSim_Labeling_o18_labeling_efficiency #end if #if $param_algorithm_RandomNumberGenerators_biological: - -algorithm:RandomNumberGenerators:biological $param_algorithm_RandomNumberGenerators_biological + -algorithm:RandomNumberGenerators:biological + #if " " in str($param_algorithm_RandomNumberGenerators_biological): + "$param_algorithm_RandomNumberGenerators_biological" + #else + $param_algorithm_RandomNumberGenerators_biological + #end if #end if #if $param_algorithm_RandomNumberGenerators_technical: - -algorithm:RandomNumberGenerators:technical $param_algorithm_RandomNumberGenerators_technical + -algorithm:RandomNumberGenerators:technical + #if " " in str($param_algorithm_RandomNumberGenerators_technical): + "$param_algorithm_RandomNumberGenerators_technical" + #else + $param_algorithm_RandomNumberGenerators_technical + #end if #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force:
--- a/readme.md Wed Mar 01 10:21:04 2017 -0500 +++ b/readme.md Tue Apr 18 15:41:04 2017 -0400 @@ -39,10 +39,10 @@ * clone or install CTD2Galaxy ```bash - git clone https://github.com/blankclemens/CTD2Galaxy.git + git clone https://github.com/WorkflowConversion/CTD2Galaxy.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. + * 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. ```bash python generator.py \ @@ -102,13 +102,6 @@ [...] ]]> ``` - * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line - - -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit - - and change it to - - -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit" * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: