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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 09:11:13 -0400
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1 Galaxy wrapper for OpenMS
2 =========================
3
4 OpenMS is an open-source software C++ library for LC/MS data management and analyses.
5 It offers an infrastructure for the rapid development of mass spectrometry related software.
6 OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux.
7
8 More informations are available at:
9
10 * https://github.com/OpenMS/OpenMS
11 * http://open-ms.sourceforge.net
12
13
14 Generating OpenMS wrappers
15 ==========================
16
17 * install OpenMS (you can do this automatically through Conda)
18 * create a folder called CTD
19 * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory:
20
21 ```bash
22 for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;
23 ```
24
25 * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow:
26
27 ```bash
28 ls >> tools.txt
29 ```
30
31 * search for the `bin` folder of your conda environment containing OpenMS and do:
32
33 ```bash
34 while read p; do
35 ./PATH/TO/BIN/$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`).
40
41 * clone or install CTDopts
42
43 ```bash
44 git clone https://github.com/genericworkflownodes/CTDopts
45 ```
46
47 * add CTDopts to your `$PYTHONPATH`
48
49 ```bash
50 export PYTHONPATH=/home/user/CTDopts/
51 ```
52
53 * clone or install CTD2Galaxy
54
55 ```bash
56 git clone https://github.com/WorkflowConversion/CTD2Galaxy.git
57 ```
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.
60
61 ```bash
62 python generator.py \
63 -i /PATH/TO/YOUR/CTD/*.ctd \
64 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \
65 -d datatypes_conf.xml -g openms \
66 -b version log debug test no_progress threads \
67 in_type executable myrimatch_executable \
68 fido_executable fidocp_executable \
69 omssa_executable pepnovo_executable \
70 xtandem_executable param_model_directory \
71 java_executable java_memory java_permgen \
72 -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \
73 -s PATH/TO/SKIP_TOOLS_FILES.txt
74 ```
75
76
77 * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example:
78
79 ```
80 sed -i '13 a\-fido_executable fido' wrappers/FidoAdapter.xml
81 sed -i '13 a\-fidocp_executable fido_choose_parameters' wrappers/FidoAdapter.xml
82 sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml
83 sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml
84 sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml
85 ```
86
87 * For some tools, additional work has to be done. In `MSGFPlusAdapter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
88
89 ```
90 <command><![CDATA[
91
92 ## check input file type
93 #set $in_type = $param_in.ext
94
95 ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files
96 ln -s '$param_in' 'param_in.${in_type}' &&
97 ln -s '$param_database' param_database.fasta &&
98 ## find location of the MSGFPlus.jar file of the msgf_plus conda package
99 MSGF_JAR=\$(msgf_plus -get_jar_path) &&
100
101 MSGFPlusAdapter
102 -executable \$MSGF_JAR
103 #if $param_in:
104 -in 'param_in.${in_type}'
105 #end if
106 #if $param_out:
107 -out $param_out
108 #end if
109 #if $param_mzid_out:
110 -mzid_out $param_mzid_out
111 #end if
112 #if $param_database:
113 -database param_database.fasta
114 #end if
115
116 [...]
117 ]]>
118 ```
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):
121
122 ```
123 <command><![CDATA[
124
125 ## check input file type
126 #set $in_type = $param_in.ext
127
128 ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
129 ln -s '$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.:
142
143 - `<data name="param_out" auto_format="true"/>`
144 - `<data name="param_out" metadata_source="param_in" auto_format="true"/>`
145
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.
147
148 ```
149 <tests>
150 <test>
151 <param name="param_in" value="DecoyDatabase_input.fasta"/>
152 <output name="param_out" file="DecoyDatabase_output.fasta"/>
153 </test>
154 </tests>
155 ```
156
157
158 * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in Galaxy-stable and are therefore in `SKIP_TOOLS_FILES.txt`:
159 * SeedListGenerator
160 * SpecLibSearcher
161 * MapAlignerIdentification
162 * MapAlignerPoseClustering
163 * MapAlignerSpectrum
164 * MapAlignerRTTransformer
165
166 * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well:
167 * OMSSAAdapter
168 * MyrimatchAdapter
169
170 * Additionally cause of a problematic parameter (-model_directory), the following adapter has been removed:
171 * PepNovoAdapter
172
173
174 Licence (MIT)
175 =============
176
177 Permission is hereby granted, free of charge, to any person obtaining a copy
178 of this software and associated documentation files (the "Software"), to deal
179 in the Software without restriction, including without limitation the rights
180 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
181 copies of the Software, and to permit persons to whom the Software is
182 furnished to do so, subject to the following conditions:
183
184 The above copyright notice and this permission notice shall be included in
185 all copies or substantial portions of the Software.
186
187 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
188 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
189 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
190 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
191 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
192 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
193 THE SOFTWARE.
194