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comparison readme.md @ 5:fdb3fbfef4cc draft

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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
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4:05f78b9d5874 5:fdb3fbfef4cc
51 ``` 51 ```
52 52
53 * clone or install CTD2Galaxy 53 * clone or install CTD2Galaxy
54 54
55 ```bash 55 ```bash
56 git clone https://github.com/WorkflowConversion/CTD2Galaxy.git 56 git clone https://github.com/WorkflowConversion/CTDConverter.git
57 ``` 57 ```
58 58
59 * 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. 59 * 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.
60 60
61 ```bash 61 ```bash
62 python generator.py \ 62 python convert.py galaxy \
63 -i /PATH/TO/YOUR/CTD/*.ctd \ 63 -i /PATH/TO/YOUR/CTD/*.ctd \
64 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ 64 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \
65 -d datatypes_conf.xml -g openms \ 65 -d datatypes_conf.xml -g openms \
66 -b version log debug test no_progress threads \ 66 -b version log debug test no_progress threads \
67 in_type executable myrimatch_executable \ 67 in_type executable myrimatch_executable \
68 fido_executable fidocp_executable \ 68 fido_executable fidocp_executable \
69 omssa_executable pepnovo_executable \ 69 omssa_executable pepnovo_e xecutable \
70 xtandem_executable param_model_directory \ 70 xtandem_executable param_model_directory \
71 java_executable java_memory java_permgen \ 71 java_executable java_memory java_permgen \
72 r_executable rt_concat_trafo_out param_id_pool \ 72 r_executable rt_concat_trafo_out param_id_pool \
73 -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ 73 -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \
74 -s PATH/TO/SKIP_TOOLS_FILES.txt 74 -s PATH/TO/tools_blacklist.txt
75 ``` 75 ```
76 76
77 77
78 * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: 78 * 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:
79 79
80 ``` 80 ```
81 sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml 81 sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml
82 sed -i '13 a\-fidocp_executable FidoChooseParameters' wrappers/FidoAdapter.xml 82 sed -i '13 a\-fidocp_executable FidoChooseParameters' wrappers/FidoAdapter.xml
83 sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml 83 sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml
169 </test> 169 </test>
170 </tests> 170 </tests>
171 ``` 171 ```
172 172
173 173
174 * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in 174 * `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
175 by the automatic conversion step and are therefore in `SKIP_TOOLS_FILES.txt`: 175 by the automatic conversion step and are therefore in `tools_blacklist.txt`:
176 * SeedListGenerator 176 * SeedListGenerator
177 * SpecLibSearcher 177 * SpecLibSearcher
178 * MapAlignerIdentification 178 * MapAlignerIdentification
179 * MapAlignerPoseClustering 179 * MapAlignerPoseClustering
180 * MapAlignerSpectrum 180 * MapAlignerSpectrum