Mercurial > repos > galaxyp > openms_openswathanalyzer

comparison readme.md @ 1:2473b7efa9d1 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:57:31 -0400
parents f9ead04f81ef
children adff2c1ccdc3
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0:f9ead04f81ef 1:2473b7efa9d1
12 12
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>