annotate readme.md @ 3:7f1786e1c462 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
author galaxyp
date Tue, 20 Mar 2018 14:42:51 -0400
parents 304c13ce9577
children e237cb433a92
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
1 Galaxy wrapper for OpenMS
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
2 =========================
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
3
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
4 OpenMS is an open-source software C++ library for LC/MS data management and analyses.
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
5 It offers an infrastructure for the rapid development of mass spectrometry related software.
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
6 OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux.
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
7
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
8 More informations are available at:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
9
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
10 * https://github.com/OpenMS/OpenMS
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
11 * http://open-ms.sourceforge.net
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
12
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
13
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
14 Generating OpenMS wrappers
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
15 ==========================
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
16
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
17 * install OpenMS (you can do this automatically through Conda)
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
18 * create a folder called CTD
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
19 * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
20
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
21 ```bash
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
22 for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
23 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
24
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
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:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
26
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
27 ```bash
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
28 ls >> tools.txt
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
29 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
30
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
31 * search for the `bin` folder of your conda environment containing OpenMS and do:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
32
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
33 ```bash
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
34 while read p; do
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
35 ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD;
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
36 done <tools.txt
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
37 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
38
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
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`).
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
40
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
41 * clone or install CTDopts
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
42
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
43 ```bash
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
44 git clone https://github.com/genericworkflownodes/CTDopts
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
45 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
46
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
47 * add CTDopts to your `$PYTHONPATH`
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
48
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
49 ```bash
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
50 export PYTHONPATH=/home/user/CTDopts/
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
51 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
52
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
53 * clone or install CTD2Galaxy
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
54
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
55 ```bash
2
304c13ce9577 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 0
diff changeset
56 git clone https://github.com/WorkflowConversion/CTDConverter.git
0
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
57 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
58
2
304c13ce9577 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 0
diff changeset
59 * If you have CTDopts and CTDConverter 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. Further information can be found on the CTDConverter page.
0
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
60
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
61 ```bash
2
304c13ce9577 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 0
diff changeset
62 python convert.py galaxy \
0
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
63 -i /PATH/TO/YOUR/CTD/*.ctd \
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
64 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
65 -d datatypes_conf.xml -g openms \
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
66 -b version log debug test no_progress threads \
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
67 in_type executable myrimatch_executable \
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
68 fido_executable fidocp_executable \
2
304c13ce9577 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 0
diff changeset
69 omssa_executable pepnovo_e xecutable \
0
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
70 xtandem_executable param_model_directory \
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
71 java_executable java_memory java_permgen \
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
72 r_executable rt_concat_trafo_out param_id_pool \
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
73 -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \
2
304c13ce9577 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 0
diff changeset
74 -s PATH/TO/tools_blacklist.txt
0
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
75 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
76
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
77
2
304c13ce9577 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 0
diff changeset
78 * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. Some of these tools might already be deprecated and the files might not exist:
0
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
79
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
80 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
81 sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
82 sed -i '13 a\-fidocp_executable FidoChooseParameters' wrappers/FidoAdapter.xml
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
83 sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
84 sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
85 sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
86 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
87
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
88 * 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):
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
89
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
90 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
91 <command><![CDATA[
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
92
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
93 ## check input file type
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
94 #set $in_type = $param_in.ext
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
95
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
96 ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
97 ln -s '$param_in' 'param_in.${in_type}' &&
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
98 ln -s '$param_database' param_database.fasta &&
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
99 ## find location of the MSGFPlus.jar file of the msgf_plus conda package
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
100 MSGF_JAR=\$(msgf_plus -get_jar_path) &&
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
101
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
102 MSGFPlusAdapter
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
103 -executable \$MSGF_JAR
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
104 #if $param_in:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
105 -in 'param_in.${in_type}'
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
106 #end if
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
107 #if $param_out:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
108 -out $param_out
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
109 #end if
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
110 #if $param_mzid_out:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
111 -mzid_out $param_mzid_out
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
112 #end if
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
113 #if $param_database:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
114 -database param_database.fasta
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
115 #end if
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
116
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
117 [...]
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
118 ]]>
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
119 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
120
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
121 * In Xtandem Converter and probably in others:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
122
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
123 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
124 #if str($param_missed_cleavages) != '':
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
125 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
126 This is because integers needs to be compared as string otherwise `0` becomes `false`.
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
127
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
128 * In `MetaProSIP.xml` add `R` as a requirement:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
129
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
130 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
131 <expand macro="requirements">
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
132 <requirement type="package" version="3.3.1">r-base</requirement>
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
133 </expand>
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
134 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
135
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
136 * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
137
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
138 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
139 <command><![CDATA[
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
140
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
141 ## check input file type
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
142 #set $in_type = $param_in.ext
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
143
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
144 ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
145 ln -s '$param_in' 'param_in.${in_type}' &&
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
146
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
147 IDFileConverter
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
148
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
149 #if $param_in:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
150 -in 'param_in.${in_type}'
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
151 #end if
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
152
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
153 [...]
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
154 ]]>
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
155 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
156
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
157 * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
158
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
159 - `<data name="param_out" auto_format="true"/>`
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
160 - `<data name="param_out" metadata_source="param_in" auto_format="true"/>`
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
161
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
162 * 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.
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
163
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
164 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
165 <tests>
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
166 <test>
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
167 <param name="param_in" value="DecoyDatabase_input.fasta"/>
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
168 <output name="param_out" file="DecoyDatabase_output.fasta"/>
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
169 </test>
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
170 </tests>
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
171 ```
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
172
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
173 * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
174 * OMSSAAdapter
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
175 * MyrimatchAdapter
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
176
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
177 * Additionally cause of a problematic parameter (-model_directory), the following adapter has been removed:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
178 * PepNovoAdapter
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
179
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
180
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
181 Licence (MIT)
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
182 =============
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
183
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
184 Permission is hereby granted, free of charge, to any person obtaining a copy
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
185 of this software and associated documentation files (the "Software"), to deal
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
186 in the Software without restriction, including without limitation the rights
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
187 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
188 copies of the Software, and to permit persons to whom the Software is
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
189 furnished to do so, subject to the following conditions:
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
190
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
191 The above copyright notice and this permission notice shall be included in
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
192 all copies or substantial portions of the Software.
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
193
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
194 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
195 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
196 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
197 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
198 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
199 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
200 THE SOFTWARE.
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
parents:
diff changeset
201