Mercurial > repos > tduigou > rrparser

annotate rrparser.xml @ 4:71ee7ebb4a67 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 7165071f816fde476feb2b6838d9f431c198f532
author tduigou
date Mon, 03 Apr 2023 12:45:49 +0000
parents dd0dfd2cb8a8
children ada9a9847d10
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
71ee7ebb4a67 planemo upload commit 7165071f816fde476feb2b6838d9f431c198f532
tduigou
parents: 3
diff changeset
1 <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
2 <description>Retrieve the reaction rules from RetroRules</description>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
3 <macros>
2
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
4 <token name="@VERSION_SUFFIX@">0</token>
4
71ee7ebb4a67 planemo upload commit 7165071f816fde476feb2b6838d9f431c198f532
tduigou
parents: 3
diff changeset
5 <token name="@TOOL_VERSION@">2.5.2</token>
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
6 </macros>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
7 <requirements>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
9 </requirements>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
10 <stdio>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
11 <regex match="WARNING:" level="warning" />
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
12 <regex match="ERROR:" level="fatal" />
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
13 </stdio>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
14 <command detect_errors="exit_code"><![CDATA[
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
15 python -m rrparser
2
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
16 #if str($rules.type) != "rules-file":
3
dd0dfd2cb8a8 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 2
diff changeset
17 --rules_file retrorules
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
18 --rule-type '$rules.type'
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
19 #else:
3
dd0dfd2cb8a8 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 2
diff changeset
20 --rules_file '$rules.file'
2
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
21 --input-format '$rules.input_format'
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
22 #end if
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
23 --diameters '$diameters'
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
24 --output-format csv
3
dd0dfd2cb8a8 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 2
diff changeset
25 --rules-dir "\${TMPDIR:-.}"
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
26 #if str($compress) == "true":
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
27 --outfile '$out_rules'.csv.gz
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
28 && mv '$out_rules'.csv.gz '$out_rules'
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
29 #else:
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
30 --outfile '$out_rules'
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
31 #end if
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
32 ]]></command>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
33 <inputs>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
34 <conditional name="rules">
2
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
35 <param name="type" type="select" label="Rule Type" help="Return the rules that are in reverse, forward, both direction or from an input user file">
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
36 <option value="retro" selected="True">RetroRules (retro)</option>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
37 <option value="forward">RetroRules (forward)</option>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
38 <option value="all">RetroRules (all)</option>
2
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
39 <option value="rules-file">Other reaction rules...</option>
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
40 </param>
2
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
41 <when value="rules-file">
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
42 <param name="file" type="data" format="csv" optional="False" label="Rules File" help="Filename of reaction rules"/>
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
43 <param name="input_format" type="select" optional="False" label="File format" help="Input file format (default: csv)">
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
44 <option value="csv" selected="True">csv</option>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
45 <option value="tsv">tsv</option>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
46 </param>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
47 </when>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
48 </conditional>
2
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
49 <param argument="--diameters" type="select" display="checkboxes" multiple="True" label="Select the diameters of the reactions rules" help=" Diameter of the sphere including the atoms around the reacting center (default is including all values: 2,4,6,8,10,12,14,16). The higher is the diameter, the more specific are the rules">
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
50 <option selected="true" value="2">2</option>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
51 <option selected="true" value="4">4</option>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
52 <option selected="true" value="6">6</option>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
53 <option selected="true" value="8">8</option>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
54 <option selected="true" value="10">10</option>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
55 <option selected="true" value="12">12</option>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
56 <option selected="true" value="14">14</option>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
57 <option selected="true" value="16">16</option>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
58 </param>
2
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
59 <param name="compress" type="boolean" checked="false" label="Compress output" />
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
60 </inputs>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
61 <outputs>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
62 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" >
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
63 <change_format>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
64 <when input="compress" format="tar" value="true"/>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
65 </change_format>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
66 </data>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
67 </outputs>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
68 <tests>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
69 <test>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
70 <!-- test 1: check if identical outputs are produced with default parameters-->
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
71 <output name="out_rules" md5="54806bd44f7a8414e78439e3bb99e6d8"/>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
72 </test>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
73 <test>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
74 <!-- test 2: check if identical outputs are produced with diameters=2,4,6-->
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
75 <param name="diameters" value="2,4,6"/>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
76 <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
77 </test>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
78 <test>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
79 <!-- test 3: check if identical outputs are produced with csv input rules file-->
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
80 <conditional name="rules">
2
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
81 <param name="type" value="rules-file"/>
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
82 <param name="file" value="rules_in.csv" />
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
83 </conditional>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
84 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
85 </test>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
86 </tests>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
87 <help><![CDATA[
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
88 RRulesParser
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
89 ============
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
90
2
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
91 Retrieve the reaction rules from `RetroRules <https://retrorules.org/>`_ extracted from public databases and expressed in the community-standard SMARTS (SMILES arbitrary target specification) format, augmented by a rule representation at different levels of specificity (the atomic environment around the reaction center).
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
92
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
93 The generated output is a file containing reaction rules which are generic descriptions of chemical reactions that can be used in retrosynthesis workflows (e.g. `Retrosynthesis KNIME Workflow <https://www.myexperiment.org/workflows/4987/versions/2.html>`_) in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors.
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
94
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
95 Input
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
96 -----
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
97
2
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
98 * **Rule Type**: (string) Return the rules that are in reverse, forward, both direction or from an input user file
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
99 * **rules-file**: (string) Filename of reaction rules provided in csv or tsv format.
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
100 * **input_format**: (string) input file format (csv: default, tsv)
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
101 * **diameters**: (integer list) diameter of the sphere including the atoms around the reacting center (default is including all values: 2,4,6,8,10,12,14,16). The higher is the diameter, the more specific are the rules
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
102
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
103 Ouput
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
104 -----
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
105
2
092545561208 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
106 * **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes.
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
107 ]]></help>
4
71ee7ebb4a67 planemo upload commit 7165071f816fde476feb2b6838d9f431c198f532
tduigou
parents: 3
diff changeset
108 <creator>
71ee7ebb4a67 planemo upload commit 7165071f816fde476feb2b6838d9f431c198f532
tduigou
parents: 3
diff changeset
109 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
71ee7ebb4a67 planemo upload commit 7165071f816fde476feb2b6838d9f431c198f532
tduigou
parents: 3
diff changeset
110 </creator>
1
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
111 <citations>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
112 <citation type="doi">10.1093/nar/gky940 </citation>
ea590c609fec "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
113 </citations>
4
71ee7ebb4a67 planemo upload commit 7165071f816fde476feb2b6838d9f431c198f532
tduigou
parents: 3
diff changeset
114 </tool>