Mercurial > repos > tduigou > rp2paths

annotate rp2paths.xml @ 5:bdde1d9dfaee draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/brsynth/rp2paths commit 46a1a47f6df15ce1873cde96c84b11d8a4544413
author tduigou
date Wed, 24 Jul 2024 08:44:12 +0000
parents fb5a3bd084a8
children 6b2ae398f4b0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
1 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT">
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
3 <macros>
5
bdde1d9dfaee planemo upload for repository https://github.com/brsynth/rp2paths commit 46a1a47f6df15ce1873cde96c84b11d8a4544413
tduigou
parents: 3
diff changeset
4 <token name="@TOOL_VERSION@">1.5.1</token>
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
5 </macros>
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
6 <requirements>
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
8 </requirements>
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
9 <stdio>
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
10 <regex match="TIMEOUT:" level="fatal" />
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
11 <regex match="ERROR:" level="fatal" />
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
12 <regex match="WARNING:" level="warning" />
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
13 </stdio>
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
14 <command detect_errors="exit_code"><![CDATA[
2
550f1c02caba "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
15 mkdir out &&
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
16 python -m rp2paths all
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
17 '$rp2_pathways'
2
550f1c02caba "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
18 --outdir out
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
19 --timeout '$adv.timeout' &&
5
bdde1d9dfaee planemo upload for repository https://github.com/brsynth/rp2paths commit 46a1a47f6df15ce1873cde96c84b11d8a4544413
tduigou
parents: 3
diff changeset
20 mv out/compounds.txt out/compounds.tsv &&
bdde1d9dfaee planemo upload for repository https://github.com/brsynth/rp2paths commit 46a1a47f6df15ce1873cde96c84b11d8a4544413
tduigou
parents: 3
diff changeset
21 cp out/compounds.tsv '$compounds' &&
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
22 if test -f 'out/out_paths.csv'; then
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
23 cp out/out_paths.csv '$master_pathways';
2
550f1c02caba "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
24 fi
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
25 ]]></command>
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
26 <inputs>
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
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."/>
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
28 <section name="adv" title="Advanced Options" expanded="false">
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
29 <param name="timeout" type="integer" value="1800" label="Time Out" help="Time out before killing a process (in seconds), default: 30 minutes." />
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
30 </section>
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
31 </inputs>
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
32 <outputs>
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
33 <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" />
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
34 <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" />
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
35 </outputs>
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
36 <tests>
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
37 <test>
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
38 <!-- test 1: check if identical outputs are produced with default parameters -->
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
39 <param name="rp2_pathways" value="retropath2_pathways.csv" />
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
40 <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/>
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
41 <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff"/>
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
42 </test>
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
43 </tests>
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
44 <help><![CDATA[
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
45 RP2paths
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
46 ========
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
47
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
48
5
bdde1d9dfaee planemo upload for repository https://github.com/brsynth/rp2paths commit 46a1a47f6df15ce1873cde96c84b11d8a4544413
tduigou
parents: 3
diff changeset
49 **RP2paths** extracts the set of heterologous pathways that lies in a metabolic space file outputted by the `RetroPath2.0 workflow <https://www.myexperiment.org/workflows/4987.html>`_ into individual pathways and enumerate them. This analysis is required to ensure that only pathways fulfilling all the precursor needs are retained for further analysis. This tool takes as input a retrosynthesis network in the CSV file produced by `RetroPath2.0 <https://toolshed.g2.bx.psu.edu/view/tduigou/retropath2/9c8ac9980bd6>`_ , and outputs the enumerated pathways (using EC numbers) as well as the structure of involved chemicals (as SMILES: Simplified Molecular-Input Line-Entry System) in TSV format.
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
50
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
51
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
52 .. image:: ${static_path}/images/enumerated_pathways.png
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
53 :width: 40 %
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
54 :align: center
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
55
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
56 |
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
57
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
58 Input
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
59 -----
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
60
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
61 Required information:
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
62
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
63 * **RetroPath2.0 Pathways**\ : Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis.
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
64
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
65 Advanced options:
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
66
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
67 * **Time Out**\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes.
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
68
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
69 Output
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
70 ------
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
71
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
72 * **Enumerated Pathways**\ : Describes all the indiviudal enumerated pathways that produce the compound of interest.
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
73 * **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System).
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
74 ]]></help>
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
75 <creator>
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
76 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
77 </creator>
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
78 <citations>
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
79 <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
1
2c788cd11881 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
80 </citations>
3
fb5a3bd084a8 planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 2
diff changeset
81 </tool>