Mercurial > repos > galaxyp > openms_featurelinkerlabeled
annotate tool-data/pepnovo_models.loc.sample @ 16:90a5563d9a69 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp | 
|---|---|
| date | Fri, 14 Jun 2024 21:30:23 +0000 | 
| parents | fc56e75d8b14 | 
| children | 
| rev | line source | 
|---|---|
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11
 
fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
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1 # This is a sample file distributed with Galaxy that enables tools | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
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2 # to use pepnovo models | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
3 # The file has three tab separated columns: name, value, and path. | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
4 # The idea is that there are a number of models in a directory: | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
5 # - each model directory has a unique name (columns 2 and 0) | 
| 
 
fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
6 # - each model can contain a set of models (column 1) | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
7 # | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
8 # The following example works fo the default models from | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
9 # http://proteomics.ucsd.edu/Software/PepNovo.html (just remove the comment | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
10 # chars and replace DIR_TO_PEPNOVO_MODELS) | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
11 | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
12 #default_models CID_IT_TRYP DIR_TO_PEPNOVO_MODELS | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
13 #default_models LTQ_COMP DIR_TO_PEPNOVO_MODELS | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
14 #default_models DBC4_PEAK DIR_TO_PEPNOVO_MODELS | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
15 #default_models CID_IT_TRYP_TAG5 DIR_TO_PEPNOVO_MODELS | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
16 #default_models CID_IT_TRYP_TAG6 DIR_TO_PEPNOVO_MODELS | 
| 
 
fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
17 #default_models ITDNV_PEAK DIR_TO_PEPNOVO_MODELS | 
| 
 
fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
18 #default_models CID_IT_TRYP_SCORE DIR_TO_PEPNOVO_MODELS | 
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fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
19 #default_models CID_IT_TRYP_TAG3 DIR_TO_PEPNOVO_MODELS | 
| 
 
fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
20 #default_models CID_IT_TRYP_DNVPART DIR_TO_PEPNOVO_MODELS | 
| 
 
fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
21 #default_models CID_IT_TRYP_TAG4 DIR_TO_PEPNOVO_MODELS | 
| 
 
fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
22 #default_models CID_IT_TRYP_DB DIR_TO_PEPNOVO_MODELS | 
| 
 
fc56e75d8b14
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
 
galaxyp 
parents:  
diff
changeset
 | 
23 #default_models CID_IT_TRYP_CSP DIR_TO_PEPNOVO_MODELS | 
