Mercurial > repos > galaxyp > openms_msgfplusadapter
changeset 1:06987761999d draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:40:51 -0400 |
| parents | 65a1b411e932 |
| children | c4a893feb484 |
| files | MSGFPlusAdapter.xml readme.md |
| diffstat | 2 files changed, 60 insertions(+), 37 deletions(-) [+] |
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--- a/MSGFPlusAdapter.xml Wed Mar 01 10:17:13 2017 -0500 +++ b/MSGFPlusAdapter.xml Tue Apr 18 15:40:51 2017 -0400 @@ -12,29 +12,29 @@ <expand macro="requirements"/> <command><![CDATA[ -## check input file type -#set $in_type = $param_in.ext + ## check input file type + #set $in_type = $param_in.ext -## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files -ln -s '$param_in' 'param_in.${in_type}' && -ln -s '$param_database' param_database.fasta && -## find location of the MSGFPlus.jar file of the msgf_plus conda package -MSGF_JAR=\$(msgf_plus -get_jar_path) && + ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files + ln -s '$param_in' 'param_in.${in_type}' && + ln -s '$param_database' param_database.fasta && + ## find location of the MSGFPlus.jar file of the msgf_plus conda package + MSGF_JAR=\$(msgf_plus -get_jar_path) && -MSGFPlusAdapter --executable \$MSGF_JAR -#if $param_in: - -in 'param_in.${in_type}' -#end if -#if $param_out: - -out $param_out -#end if -#if $param_mzid_out: - -mzid_out $param_mzid_out -#end if -#if $param_database: - -database param_database.fasta -#end if + MSGFPlusAdapter + -executable \$MSGF_JAR + #if $param_in: + -in 'param_in.${in_type}' + #end if + #if $param_out: + -out $param_out + #end if + #if $param_mzid_out: + -mzid_out $param_mzid_out + #end if + #if $param_database: + -database param_database.fasta + #end if #if $param_add_decoys: -add_decoys #end if @@ -42,25 +42,55 @@ -precursor_mass_tolerance $param_precursor_mass_tolerance #end if #if $param_precursor_error_units: - -precursor_error_units $param_precursor_error_units + -precursor_error_units + #if " " in str($param_precursor_error_units): + "$param_precursor_error_units" + #else + $param_precursor_error_units + #end if #end if #if $param_isotope_error_range: -isotope_error_range "$param_isotope_error_range" #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_instrument: - -instrument $param_instrument + -instrument + #if " " in str($param_instrument): + "$param_instrument" + #else + $param_instrument + #end if #end if #if $param_enzyme: - -enzyme $param_enzyme + -enzyme + #if " " in str($param_enzyme): + "$param_enzyme" + #else + $param_enzyme + #end if #end if #if $param_protocol: - -protocol $param_protocol + -protocol + #if " " in str($param_protocol): + "$param_protocol" + #else + $param_protocol + #end if #end if #if $param_tryptic: - -tryptic $param_tryptic + -tryptic + #if " " in str($param_tryptic): + "$param_tryptic" + #else + $param_tryptic + #end if #end if #if $param_min_precursor_charge: -min_precursor_charge $param_min_precursor_charge @@ -113,7 +143,7 @@ -force #end if #end if -]]> + ]]> </command> <inputs> <param name="param_in" type="data" format="mzxml,mgf,mzml" optional="False" label="Input file (MS-GF+ parameter '-s')" help="(-in) "/>
--- a/readme.md Wed Mar 01 10:17:13 2017 -0500 +++ b/readme.md Tue Apr 18 15:40:51 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.: