Mercurial > repos > galaxyp > openms_speclibcreator
comparison readme.md @ 1:c61d23e4f90e draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author | galaxyp |
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date | Wed, 09 Aug 2017 09:24:49 -0400 |
parents | 564a6acb89e8 |
children | 14d957693235 |
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13 | 13 |
14 Generating OpenMS wrappers | 14 Generating OpenMS wrappers |
15 ========================== | 15 ========================== |
16 | 16 |
17 * install OpenMS (you can do this automatically through the Tool Shed) | 17 * install OpenMS (you can do this automatically through Conda) |
18 * create a folder called CTD | 18 * create a folder called CTD |
19 * inside of your new installed openms/bin folder, execute the following command: | 19 * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory: |
20 | 20 |
21 ```bash | 21 ```bash |
22 for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; | 22 for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; |
23 ``` | 23 ``` |
24 | 24 |
25 * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`). | 25 * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow: |
26 | |
27 ```bash | |
28 ls >> tools.txt | |
29 ``` | |
30 | |
31 * search for the `bin` folder of your conda environment containing OpenMS and do: | |
32 | |
33 ```bash | |
34 while read p; do | |
35 ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD; | |
36 done <tools.txt | |
37 ``` | |
38 | |
39 * You should have all CTD files now. `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`). | |
26 | 40 |
27 * clone or install CTDopts | 41 * clone or install CTDopts |
28 | 42 |
29 ```bash | 43 ```bash |
30 git clone https://github.com/genericworkflownodes/CTDopts | 44 git clone https://github.com/genericworkflownodes/CTDopts |
37 ``` | 51 ``` |
38 | 52 |
39 * clone or install CTD2Galaxy | 53 * clone or install CTD2Galaxy |
40 | 54 |
41 ```bash | 55 ```bash |
42 git clone https://github.com/blankclemens/CTD2Galaxy.git | 56 git clone https://github.com/WorkflowConversion/CTD2Galaxy.git |
43 ``` | 57 ``` |
44 | 58 |
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. | 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. |
46 | 60 |
47 ```bash | 61 ```bash |
48 python generator.py \ | 62 python generator.py \ |
49 -i /PATH/TO/YOUR/CTD/*.ctd \ | 63 -i /PATH/TO/YOUR/CTD/*.ctd \ |
50 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ | 64 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ |
100 #end if | 114 #end if |
101 | 115 |
102 [...] | 116 [...] |
103 ]]> | 117 ]]> |
104 ``` | 118 ``` |
105 * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line | 119 |
120 * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): | |
106 | 121 |
107 -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit | 122 ``` |
108 | 123 <command><![CDATA[ |
109 and change it to | |
110 | 124 |
111 -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit" | 125 ## check input file type |
126 #set $in_type = $param_in.ext | |
112 | 127 |
113 * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: | 128 ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files |
129 ln -s '$param_in' 'param_in.${in_type}' && | |
130 | |
131 IDFileConverter | |
132 | |
133 #if $param_in: | |
134 -in 'param_in.${in_type}' | |
135 #end if | |
136 | |
137 [...] | |
138 ]]> | |
139 ``` | |
140 | |
141 * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.: | |
114 | 142 |
115 <data name="param_out" metadata_source="param_in" auto_format="true"/> | 143 - `<data name="param_out" auto_format="true"/>` |
144 - `<data name="param_out" metadata_source="param_in" auto_format="true"/>` | |
116 | 145 |
117 * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files. | 146 * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files. |
118 | 147 |
119 ``` | 148 ``` |
120 <tests> | 149 <tests> |