Mercurial > repos > galaxyp > openms_featurefindermultiplex
annotate readme.md @ 16:9876bda3ec53 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 18:59:52 +0000 |
parents | 3098bea02bd8 |
children | c9b2a5022d9e |
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14e0f052de8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 Galaxy wrapper for OpenMS |
14e0f052de8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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2 ========================= |
14e0f052de8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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3 |
14e0f052de8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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4 OpenMS is an open-source software C++ library for LC/MS data management and analyses. |
14e0f052de8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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5 It offers an infrastructure for the rapid development of mass spectrometry related software. |
14e0f052de8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux. |
14e0f052de8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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7 |
14e0f052de8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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8 More informations are available at: |
14e0f052de8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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9 |
14e0f052de8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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10 * https://github.com/OpenMS/OpenMS |
12
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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11 * https://www.openms.de/ |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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12 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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13 The wrappers for these tools and most of their tests are automatically |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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14 generated using the `generate.sh` script. The generation of the tools is |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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15 based on the CTDConverter (https://github.com/WorkflowConversion/CTDConverter) |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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16 which can be fine tuned via the `hardcoded_params.json` file. This file allows |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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17 to blacklist and hardcode parameters and to modify or set arbitrary |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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18 CTD/XML attributes. |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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19 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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20 Note that, due to its size, the test data is excluded from this repository. In |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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21 order to generate the test data on call `test-data.sh`. |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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22 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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23 Manual updates should only be done to |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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24 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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25 - and the manually contributed tests in `macros_test.xml` (The goal is that all |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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26 tools that do not have an automatically generated test are covered here) |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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27 - the `hardcoded_params.json` files |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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28 |
16
9876bda3ec53
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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29 Wrapper versions are managed in `bump.json`. For tools listed in the file |
9876bda3ec53
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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30 the wrapper version will be set accordingly and otherwise `0` is used. |
9876bda3ec53
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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31 For a major update of the tool version the bump file should be reset (to `{}`). |
9876bda3ec53
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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32 |
12
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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33 In a few cases patches may be acceptable. |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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34 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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35 Installation |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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36 ============ |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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37 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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38 The Galaxy OpenMS tools can be installed from the toolshed. While most tools |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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39 will work out of the box some need attention since requirements can not be |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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40 fulfilled via Conda: |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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41 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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42 Not yet in Conda are: |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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43 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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44 - SpectraST (http://tools.proteomecenter.org/wiki/index.php?title=SpectraST) |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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45 - MaRaCluster (https://github.com/statisticalbiotechnology/maracluster) |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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46 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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47 Binaries for these tools can easily be obtained via: |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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48 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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49 ``` |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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50 VERSION=.... |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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51 git git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git OpenMS$VERSION.0-git |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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52 git submodule init OpenMS$VERSION.0-git |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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53 git submodule update OpenMS$VERSION.0-git |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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54 ``` |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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55 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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56 They are located in `OpenMS$VERSION-git/THIRDPARTY/`. |
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14e0f052de8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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57 |
12
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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58 Not in Conda due to licencing restrictions: |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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59 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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60 - Mascot http://www.matrixscience.com/ |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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61 - MSFragger https://github.com/Nesvilab/MSFragger |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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62 - Novor http://www.rapidnovor.org/novor |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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63 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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64 There are multiple ways to enable the Galaxy tools to use these binaries. |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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65 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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66 - Just copy them to the `bin` path within Galaxy's conda environment |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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67 - Put them in any other path that that is included in PATH |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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68 - Edit the corresponding tools: In the command line part search for the parameters `-executable`, `-maracluster_executable`, or `-mascot_directory` and edit them appropriately. |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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69 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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70 Working |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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71 ======= |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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72 |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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73 The tools work by: |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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74 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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75 Preprocessing: |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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76 |
3098bea02bd8
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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77 - For input data set parameters the links to the actual location of the data |
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9876bda3ec53
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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78 sets are created, the link names are `element_identifier`.`EXT`, where `EXT` |
9876bda3ec53
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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79 is an extension that is known by OpenMS |
9876bda3ec53
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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80 - In order to avoid name collisions for the created links each is placed in a |
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81 unique directory: `PARAM_NAME/DATASET_ID`, where `PARAM_NAME` is the name |
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82 of the parameter and `DATASET_ID` is the id of the Galaxy dataset |
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83 - the same happens for output parameters that are in 1:1 correspondence with |
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84 an input parameter |
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85 |
12
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86 |
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87 Main: |
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88 |
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89 - The galaxy wrapper create two json config files: one containing the |
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90 parameters and the values chosen by the user and the other the values of |
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91 hardcoded parameters. |
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92 - With `OpenMSTool -write_ctd ./` a CTD (names OpenMSTool.ctd) file is |
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93 generated that contains the default values. |
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94 - A call to `fill_ctd.py` fills in the values from the json config files into |
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95 the CTD file |
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96 - The actual tool is called `OpenMSTool -ini OpenMSTool.ctd` and also all input |
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97 and output parameters are given on the command line. |
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98 |
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99 Postprocessing: |
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100 |
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101 - output data sets are moved to the final locations |
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102 |
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103 Note: The reason for handling data sets on the command line (and not specifying |
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104 them in the CTD file) is mainly that all files in Galaxy have the extension |
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105 `.dat` and OpenMS tools require an appropriate extension. But this may change |
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106 in the future. |
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107 |
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108 Generating OpenMS wrappers |
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109 ========================== |
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110 |
12
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111 1. remove old test data: `rm -rf $(ls -d test-data/* | egrep -v "random|\.loc")` |
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112 2. `./generate.sh` |
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113 |
12
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114 Whats happening: |
0
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115 |
12
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116 1. The binaries of the OpenMS package can generate a CTD file that describes |
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117 the parameters. These CTD files are converted to xml Galaxy tool descriptions |
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118 using the `CTDConverter`. |
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119 |
12
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120 2. The CI testing framework of OpenMS contains command lines and test data |
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121 (https://github.com/OpenMS/OpenMS/tree/develop/src/tests/topp). These tests |
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122 are described in two CMake files. |
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123 |
12
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124 - From these CMake files Galaxy tests are auto generated and stored in `macros_autotest.xml` |
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125 - The command lines are stored in `prepare_test_data.sh` for regeneration of test data |
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126 |
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127 More details can be found in the comments of the shell script. |
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128 |
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129 Open problems |
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130 ============= |
0
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131 |
12
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132 Some tools stall in CI testing using `--biocontainers` which is why the OpenMS |
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133 tools are currently listed in `.tt_biocontainer_skip`. This is |
0
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134 |
12
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135 - AssayGeneratorMetabo and SiriusAdapter (both depend on sirius) |
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136 - OMSSAAdapter |
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137 |
12
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138 Using `docker -t` seems to solve the problem (see |
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139 https://github.com/galaxyproject/galaxy/issues/10153). |
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140 |
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141 Licence (MIT) |
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142 ============= |
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143 |
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144 Permission is hereby granted, free of charge, to any person obtaining a copy |
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145 of this software and associated documentation files (the "Software"), to deal |
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146 in the Software without restriction, including without limitation the rights |
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147 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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148 copies of the Software, and to permit persons to whom the Software is |
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149 furnished to do so, subject to the following conditions: |
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150 |
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151 The above copyright notice and this permission notice shall be included in |
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152 all copies or substantial portions of the Software. |
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153 |
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154 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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155 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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156 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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157 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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158 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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159 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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160 THE SOFTWARE. |
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161 |