Mercurial > repos > galaxyp > openms_metaprosip
changeset 5:fdb3fbfef4cc draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
| author | galaxyp |
|---|---|
| date | Mon, 12 Feb 2018 12:54:44 -0500 |
| parents | 05f78b9d5874 |
| children | 96cc79adfadb |
| files | MetaProSIP.xml SKIP_TOOLS_FILE.txt macros.xml readme.md tools_blacklist.txt |
| diffstat | 5 files changed, 24 insertions(+), 27 deletions(-) [+] |
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--- a/MetaProSIP.xml Thu Jan 11 17:59:18 2018 -0500 +++ b/MetaProSIP.xml Mon Feb 12 12:54:44 2018 -0500 @@ -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: [Utilities]--> -<tool id="MetaProSIP" name="MetaProSIP" version="2.2.0.1"> +<tool id="MetaProSIP" name="MetaProSIP" version="2.3.0"> <description>Performs proteinSIP on peptide features for elemental flux analysis.</description> <macros> <token name="@EXECUTABLE@">MetaProSIP</token> @@ -10,7 +10,7 @@ <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"> - <requirement type="package" version="3.3.1">r-base</requirement> + <requirement type="package" version="3.4.1">r-base</requirement> </expand> <command>MetaProSIP @@ -29,9 +29,6 @@ #if $param_in_featureXML: -in_featureXML $param_in_featureXML #end if - --r_executable 'R' - #if $param_mz_tolerance_ppm: -mz_tolerance_ppm $param_mz_tolerance_ppm #end if @@ -140,7 +137,7 @@ <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/> <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/> <param name="param_xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="(-xic_threshold) If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/> - <param name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R^2 of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/> + <param name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R² of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/> <param name="param_weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help="(-weight_merge_window) "/> <param name="param_plot_extension" display="radio" type="select" optional="False" value="png" label="Extension used for plots (png|svg|pdf)" help="(-plot_extension) "> <option value="png" selected="true">png</option> @@ -191,5 +188,5 @@ <help>Performs proteinSIP on peptide features for elemental flux analysis. -For more information, visit http://www.openms.de/comp/metaprosip/</help> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaProSIP.html</help> </tool>
--- a/SKIP_TOOLS_FILE.txt Thu Jan 11 17:59:18 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -OMSSAAdapter -MyriMatchAdapter -PepNovoAdapter -SeedListGenerator -SpecLibSearcher -MapAlignerIdentification -MapAlignerPoseClustering -MapAlignerSpectrum -MapAlignerRTTransformer
--- a/macros.xml Thu Jan 11 17:59:18 2018 -0500 +++ b/macros.xml Mon Feb 12 12:54:44 2018 -0500 @@ -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>
--- a/readme.md Thu Jan 11 17:59:18 2018 -0500 +++ b/readme.md Mon Feb 12 12:54:44 2018 -0500 @@ -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