Mercurial > repos > galaxyp > openms_decoydatabase

comparison readme.md @ 1:bf3b4e5c0dcb draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author galaxyp
date Tue, 18 Apr 2017 16:01:49 -0400
parents 53f456ded5a6
children 8ced1ef014ae
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0:53f456ded5a6 1:bf3b4e5c0dcb
37 ``` 37 ```
38 38
39 * clone or install CTD2Galaxy 39 * clone or install CTD2Galaxy
40 40
41 ```bash 41 ```bash
42 git clone https://github.com/blankclemens/CTD2Galaxy.git 42 git clone https://github.com/WorkflowConversion/CTD2Galaxy.git
43 ``` 43 ```
44 44
45 * 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. 45 * 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.
46 46
47 ```bash 47 ```bash
48 python generator.py \ 48 python generator.py \
49 -i /PATH/TO/YOUR/CTD/*.ctd \ 49 -i /PATH/TO/YOUR/CTD/*.ctd \
50 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ 50 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \
100 #end if 100 #end if
101 101
102 [...] 102 [...]
103 ]]> 103 ]]>
104 ``` 104 ```
105 * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line
106
107 -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit
108
109 and change it to
110
111 -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit"
112 105
113 * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: 106 * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
114 107
115 <data name="param_out" metadata_source="param_in" auto_format="true"/> 108 <data name="param_out" metadata_source="param_in" auto_format="true"/>
116 109