| Previous changeset 6:e64a9dc50d1c (2018-01-11) Next changeset 8:92d0f39d9b8f (2018-03-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b |
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modified:
IDFileConverter.xml macros.xml readme.md |
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added:
tools_blacklist.txt |
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removed:
SKIP_TOOLS_FILE.txt |
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| diff -r e64a9dc50d1c -r 1dcffdad49c0 IDFileConverter.xml --- a/IDFileConverter.xml Thu Jan 11 17:47:21 2018 -0500 +++ b/IDFileConverter.xml Mon Feb 12 13:07:53 2018 -0500 |
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| @@ -1,7 +1,7 @@ <?xml version='1.0' encoding='UTF-8'?> -<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [ID Processing]--> -<tool id="IDFileConverter" name="IDFileConverter" version="2.2.0"> +<tool id="IDFileConverter" name="IDFileConverter" version="2.3.0"> <description>Converts identification engine file formats.</description> <macros> <token name="@EXECUTABLE@">IDFileConverter</token> @@ -10,19 +10,19 @@ <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> - <command><![CDATA[ + <command><![CDATA[ -## check input file type -#set $in_type = $param_in.ext + ## check input file type + #set $in_type = $param_in.ext -## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files -ln -s '$param_in' 'param_in.${in_type}' && + ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files + ln -s '$param_in' 'param_in.${in_type}' && -IDFileConverter + IDFileConverter -#if $param_in: - -in 'param_in.${in_type}' -#end if + #if $param_in: + -in 'param_in.${in_type}' + #end if #if $param_out: -out $param_out #end if @@ -61,6 +61,9 @@ #if $adv_opts.param_no_spectra_data_override: -no_spectra_data_override #end if + #if $adv_opts.param_add_ionmatch_annotation: + -add_ionmatch_annotation $adv_opts.param_add_ionmatch_annotation +#end if #if $adv_opts.param_force: -force #end if @@ -101,6 +104,7 @@ </sanitizer> </param> <param name="param_no_spectra_data_override" display="radio" type="boolean" truevalue="-no_spectra_data_override" falsevalue="" checked="false" optional="True" label="[+mz_file only] Setting this flag will avoid overriding 'spectra_data' in ProteinIdentifications if mz_file is given and 'spectrum_reference's are added/updated" help="(-no_spectra_data_override) Use only if you are sure it is absolutely the same mz_file as used for identification"/> + <param name="param_add_ionmatch_annotation" type="float" value="0.0" label="[+mz_file only] Will annotate the contained identifications with their matches in the given mz_file" help="(-add_ionmatch_annotation) Will take quite some while. Match tolerance is .4"/> <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> </expand> </inputs> |
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| diff -r e64a9dc50d1c -r 1dcffdad49c0 SKIP_TOOLS_FILE.txt --- a/SKIP_TOOLS_FILE.txt Thu Jan 11 17:47:21 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -OMSSAAdapter -MyriMatchAdapter -PepNovoAdapter -SeedListGenerator -SpecLibSearcher -MapAlignerIdentification -MapAlignerPoseClustering -MapAlignerSpectrum -MapAlignerRTTransformer |
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| diff -r e64a9dc50d1c -r 1dcffdad49c0 macros.xml --- a/macros.xml Thu Jan 11 17:47:21 2018 -0500 +++ b/macros.xml Mon Feb 12 13:07:53 2018 -0500 |
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| @@ -2,10 +2,10 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.2">openms</requirement> + <requirement type="package" version="2.3">openms</requirement> <requirement type="package" version="15.12.15.2">xtandem</requirement> <requirement type="package" version="1.0">fido</requirement> - <requirement type="package" version="2016.10.26">msgf_plus</requirement> + <requirement type="package" version="2017.07.21">msgf_plus</requirement> <yield/> </requirements> </xml> |
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| diff -r e64a9dc50d1c -r 1dcffdad49c0 readme.md --- a/readme.md Thu Jan 11 17:47:21 2018 -0500 +++ b/readme.md Mon Feb 12 13:07:53 2018 -0500 |
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| @@ -53,29 +53,29 @@ * clone or install CTD2Galaxy ```bash - git clone https://github.com/WorkflowConversion/CTD2Galaxy.git + git clone https://github.com/WorkflowConversion/CTDConverter.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. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it. + * If you have CTDopts and CTDConverter 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. You might have to install `libxslt` and `lxml` to run it. Further information can be found on the CTDConverter page. ```bash - python generator.py \ + python convert.py galaxy \ -i /PATH/TO/YOUR/CTD/*.ctd \ -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ -d datatypes_conf.xml -g openms \ -b version log debug test no_progress threads \ in_type executable myrimatch_executable \ fido_executable fidocp_executable \ - omssa_executable pepnovo_executable \ + omssa_executable pepnovo_e xecutable \ xtandem_executable param_model_directory \ java_executable java_memory java_permgen \ r_executable rt_concat_trafo_out param_id_pool \ -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ - -s PATH/TO/SKIP_TOOLS_FILES.txt + -s PATH/TO/tools_blacklist.txt ``` - * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: + * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. Some of these tools might already be deprecated and the files might not exist: ``` sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml @@ -171,8 +171,8 @@ ``` - * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in - by the automatic conversion step and are therefore in `SKIP_TOOLS_FILES.txt`: + * `This section might not be up to date. It might be worth trying if these tools will run now.` These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in + by the automatic conversion step and are therefore in `tools_blacklist.txt`: * SeedListGenerator * SpecLibSearcher * MapAlignerIdentification |
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| diff -r e64a9dc50d1c -r 1dcffdad49c0 tools_blacklist.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools_blacklist.txt Mon Feb 12 13:07:53 2018 -0500 |
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| @@ -0,0 +1,9 @@ +OMSSAAdapter +MyriMatchAdapter +PepNovoAdapter +SeedListGenerator +SpecLibSearcher +MapAlignerIdentification +MapAlignerPoseClustering +MapAlignerSpectrum +MapAlignerRTTransformer |