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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:39:28 -0500
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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 the Tool Shed)
18 * create a folder called CTD
19 * inside of your new installed openms/bin folder, execute the following command:
20
21 ```bash
22 for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;
23 ```
24
25 * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`).
26
27 * clone or install CTDopts
28
29 ```bash
30 git clone https://github.com/genericworkflownodes/CTDopts
31 ```
32
33 * add CTDopts to your `$PYTHONPATH`
34
35 ```bash
36 export PYTHONPATH=/home/user/CTDopts/
37 ```
38
39 * clone or install CTD2Galaxy
40
41 ```bash
42 git clone https://github.com/blankclemens/CTD2Galaxy.git
43 ```
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.
46
47 ```bash
48 python generator.py \
49 -i /PATH/TO/YOUR/CTD/*.ctd \
50 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \
51 -d datatypes_conf.xml -g openms \
52 -b version log debug test no_progress threads \
53 in_type executable myrimatch_executable \
54 fido_executable fidocp_executable \
55 omssa_executable pepnovo_executable \
56 xtandem_executable param_model_directory \
57 java_executable java_memory java_permgen \
58 -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \
59 -s PATH/TO/SKIP_TOOLS_FILES.txt
60 ```
61
62
63 * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example:
64
65 ```
66 sed -i '13 a\-fido_executable fido' wrappers/FidoAdapter.xml
67 sed -i '13 a\-fidocp_executable fido_choose_parameters' wrappers/FidoAdapter.xml
68 sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml
69 sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml
70 sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml
71 ```
72
73 * 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):
74
75 ```
76 <command><![CDATA[
77
78 ## check input file type
79 #set $in_type = $param_in.ext
80
81 ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files
82 ln -s '$param_in' 'param_in.${in_type}' &&
83 ln -s '$param_database' param_database.fasta &&
84 ## find location of the MSGFPlus.jar file of the msgf_plus conda package
85 MSGF_JAR=\$(msgf_plus -get_jar_path) &&
86
87 MSGFPlusAdapter
88 -executable \$MSGF_JAR
89 #if $param_in:
90 -in 'param_in.${in_type}'
91 #end if
92 #if $param_out:
93 -out $param_out
94 #end if
95 #if $param_mzid_out:
96 -mzid_out $param_mzid_out
97 #end if
98 #if $param_database:
99 -database param_database.fasta
100 #end if
101
102 [...]
103 ]]>
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
113 * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
114
115 <data name="param_out" metadata_source="param_in" auto_format="true"/>
116
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.
118
119 ```
120 <tests>
121 <test>
122 <param name="param_in" value="DecoyDatabase_input.fasta"/>
123 <output name="param_out" file="DecoyDatabase_output.fasta"/>
124 </test>
125 </tests>
126 ```
127
128
129 * 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`:
130 * SeedListGenerator
131 * SpecLibSearcher
132 * MapAlignerIdentification
133 * MapAlignerPoseClustering
134 * MapAlignerSpectrum
135 * MapAlignerRTTransformer
136
137 * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well:
138 * OMSSAAdapter
139 * MyrimatchAdapter
140
141 * Additionally cause of a problematic parameter (-model_directory), the following adapter has been removed:
142 * PepNovoAdapter
143
144
145 Licence (MIT)
146 =============
147
148 Permission is hereby granted, free of charge, to any person obtaining a copy
149 of this software and associated documentation files (the "Software"), to deal
150 in the Software without restriction, including without limitation the rights
151 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
152 copies of the Software, and to permit persons to whom the Software is
153 furnished to do so, subject to the following conditions:
154
155 The above copyright notice and this permission notice shall be included in
156 all copies or substantial portions of the Software.
157
158 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
159 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
160 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
161 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
162 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
163 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
164 THE SOFTWARE.
165