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comparison rp2paths.xml @ 6:6b2ae398f4b0 draft

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planemo upload for repository https://github.com/brsynth/rp2paths commit 0718e1c463ce94ee76679ec10db8bc839a9a3199-dirty
author tduigou
date Fri, 03 Oct 2025 11:16:40 +0000
parents bdde1d9dfaee
children f3843f6b7332
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5:bdde1d9dfaee 6:6b2ae398f4b0
1 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT"> 1 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT">
2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description> 2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.5.1</token> 4 <token name="@TOOL_VERSION@">2.1.0</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>
8 </requirements> 8 </requirements>
9 <stdio> 9 <stdio>
10 <regex match="TIMEOUT:" level="fatal" /> 10 <regex match="TIMEOUT:" level="fatal" />
11 <regex match="ERROR:" level="fatal" /> 11 <regex match="ERROR:" level="fatal" />
12 <regex match="WARNING:" level="warning" /> 12 <regex match="WARNING:" level="warning" />
13 </stdio> 13 </stdio>
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 mkdir out && 15 mkdir out &&
16 python -m rp2paths all 16 python -m rp2paths all
17 '$rp2_pathways' 17 '$rp2_pathways'
18 --outdir out 18 --outdir out
19 --timeout '$adv.timeout' && 19 --timeout '$adv.timeout'
20 #if str($adv.forward) == 'true'
21 --forward
22 #end if
23 #if $adv.cofile
24 --cofile '$adv.cofile'
25 #end if
26 #if str($adv.mindepth) == 'true'
27 --minDepth
28 #end if
29 #if $adv.sink
30 --customsinkfile '$adv.sink'
31 #end if
32 --maxsteps '$adv.maxsteps'
33 --maxpaths '$adv.maxpaths'
34 #if str($adv.unfold) == 'true'
35 --unfold_compounds
36 #end if
37 #set cmp_ids = []
38 #for $x in $adv.rep_include_path
39 #silent cmp_ids.append(str($x.cmp_id))
40 #end for
41 #if len(cmp_ids) > 0
42 #set cmp_id = ' '.join($cmp_ids)
43 --onlyPathsStartingBy $cmp_id
44 #end if
45 #set cmp_ids = []
46 #for $x in $adv.rep_exclude_path
47 #silent cmp_ids.append(str($x.cmp_id))
48 #end for
49 #if len(cmp_ids) > 0
50 #set cmp_id = ' '.join($cmp_ids)
51 --notPathsStartingBy $cmp_id
52 #end if
53 #if $adv.cmpfile
54 --cmpdnamefile '$adv.cmpfile'
55 #end if
56 --target '$adv.target' &&
20 mv out/compounds.txt out/compounds.tsv && 57 mv out/compounds.txt out/compounds.tsv &&
21 cp out/compounds.tsv '$compounds' && 58 cp out/compounds.tsv '$compounds' &&
22 if test -f 'out/out_paths.csv'; then 59 if test -f 'out/out_paths.csv'; then
23 cp out/out_paths.csv '$master_pathways'; 60 cp out/out_paths.csv '$master_pathways';
24 fi 61 fi
25 ]]></command> 62 ]]></command>
26 <inputs> 63 <inputs>
27 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" help="Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis."/> 64 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways"
65 help="Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis." />
28 <section name="adv" title="Advanced Options" expanded="false"> 66 <section name="adv" title="Advanced Options" expanded="false">
29 <param name="timeout" type="integer" value="1800" label="Time Out" help="Time out before killing a process (in seconds), default: 30 minutes." /> 67 <param name="timeout" type="integer" value="1800" label="Time Out"
68 help="Time out before killing a process (in seconds), default: 30 minutes." />
69 <param
70 name="forward" type="boolean" checked="false" label="Forward"
71 help="Consider reactions in the forward direction" />
72 <param name="cofile"
73 type="data" format="csv" optional="True" label="List of cofactors" />
74 <param
75 name="mindepth" type="boolean" checked="false" label="Minimal depth scope"
76 help="Use minimal depth scope, i.e. stop the scope computation as as soon an a first minimal path linking target to sink is found" />
77 <param
78 name="sink" type="data" format="tabular" optional="True" label="List of sinks"
79 help="Listing compounds to consider as sink compounds. Sink compounds should be provided by their IDs, as used in the reaction.erxn file" />
80 <param
81 name="maxsteps" type="integer" min="0" value="0" max="20" label="Max steps"
82 help="Cutoff on the maximum number of steps in a pathways. 0 (default) for unlimited number of steps" />
83 <param
84 name="maxpaths" type="integer" min="0" value="0" max="20" label="Max pathways"
85 help="Cutoff on the maximum number of pathways. 0 (default) for unlimited number of pathways" />
86 <param
87 name="unfold" type="boolean" checked="false" label="Unfold pathways"
88 help="Unfold pathways based on equivalencie of compounds (can lead to combinatorial explosion)." />
89 <repeat name="rep_include_path" title="Include path starting by">
90 <param name="cmp_id" type="text" label="Path label"
91 help="List of compounds IDs to consider. If specified, only paths making use of at least one of these compounds as initial substrate (first step of a pathway) are kept.">
92 <validator type="empty_field" message="Not empty" />
93 </param>
94 </repeat>
95 <repeat name="rep_exclude_path" title="Include path starting by">
96 <param name="cmp_id" type="text" label="Path label"
97 help="List of compounds IDs. If specifed, paths making use of one of these compounds as unique initial substrate will be filtered out">
98 <validator type="empty_field" message="Not empty" />
99 </param>
100 </repeat>
101 <param name="cmpfile" type="data" format="tabular"
102 optional="True" label="List of compounds" help="File with name of compounds" />
103 <param
104 name="target" type="text" value="TARGET_0000000001"
105 label="Target compound internal ID"
106 help="This internal ID specifies which compound should be considered as the targeted compound. The default behavior is to consider as the target the first compound used as a source compound in a first iteration of a metabolic exploration. Let this value as it is except if you know what you are doing" />
30 </section> 107 </section>
31 </inputs> 108 </inputs>
32 <outputs> 109 <outputs>
33 <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" /> 110 <data name="master_pathways" format="csv"
34 <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" /> 111 label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" />
112 <data name="compounds" format="tabular"
113 label="${tool.name} on ${rp2_pathways.name} : Compounds" />
35 </outputs> 114 </outputs>
36 <tests> 115 <tests>
37 <test> 116 <test>
38 <!-- test 1: check if identical outputs are produced with default parameters --> 117 <!-- test 1: check if identical outputs are produced with default parameters -->
39 <param name="rp2_pathways" value="retropath2_pathways.csv" /> 118 <param name="rp2_pathways" value="retropath2_pathways.csv" />
40 <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/> 119 <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff" />
41 <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff"/> 120 <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff" />
42 </test> 121 </test>
43 </tests> 122 </tests>
44 <help><![CDATA[ 123 <help><![CDATA[
45 RP2paths 124 RP2paths
46 ======== 125 ========
53 :width: 40 % 132 :width: 40 %
54 :align: center 133 :align: center
55 134
56 | 135 |
57 136
58 Input
59 -----
60
61 Required information:
62
63 * **RetroPath2.0 Pathways**\ : Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis.
64
65 Advanced options:
66
67 * **Time Out**\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes.
68
69 Output 137 Output
70 ------ 138 ------
71 139
72 * **Enumerated Pathways**\ : Describes all the indiviudal enumerated pathways that produce the compound of interest. 140 * **Enumerated Pathways**\ : Describes all the indiviudal enumerated pathways that produce the compound of interest.
73 * **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System). 141 * **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System).
74 ]]></help> 142 ]]></help>
75 <creator> 143 <creator>
76 <organization name="BioRetroSynth" url="https://github.com/brsynth"/> 144 <organization name="BioRetroSynth" url="https://github.com/brsynth" />
77 </creator> 145 </creator>
78 <citations> 146 <citations>
79 <citation type="doi">10.1016/j.ymben.2017.12.002</citation> 147 <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
80 </citations> 148 </citations>
81 </tool> 149 </tool>