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comparison rpcompletion.xml @ 0:98d925a75257 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Tue, 23 Nov 2021 13:45:45 +0000
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1 <tool id="rpCompletion" name="Complete Reactions" version="5.9.2">
2 <description>From the output of RP2Paths and RetroPath2.0, generate SBML unique and complete (with cofactors) pathways with mono-component reactions</description>
3 <requirements>
4 <requirement type="package" version="5.9.2">rptools</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1" level="fatal" description="Could not Xref compartment_id" />
8 <exit_code range="2" level="fatal" description="ValueError returned" />
9 </stdio>
10 <command detect_errors="exit_code"><![CDATA[
11 python -m rptools.rpcompletion
12 '$rp2_pathways'
13 '$sink'
14 '$rp2paths_compounds'
15 '$rp2paths_pathways'
16 completed_pathways
17 --upper_flux_bound '$adv.upper_flux_bound'
18 --lower_flux_bound '$adv.lower_flux_bound'
19 --max_subpaths_filter '$adv.max_subpaths_filter'
20 ]]></command>
21 <inputs>
22 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
23 <param name="rp2paths_compounds" type="data" format="tsv" label="RP2paths compounds" />
24 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
25 <param name="sink" type="data" format="csv" label="Sink from SBML" />
26 <section name="adv" title="Advanced Options" expanded="false">
27 <param name="max_subpaths_filter" type="integer" value="10" label="Max subpaths generated per pathway" />
28 <param name="upper_flux_bound" type="integer" value="999999" label="Upper flux bound" />
29 <param name="lower_flux_bound" type="integer" value="0" label="Lower flux bound" />
30 </section>
31 </inputs>
32 <outputs>
33 <collection name="pathways" type="list" label="${tool.name}">
34 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml" format="xml" directory="completed_pathways" visible="false" />
35 </collection>
36 </outputs>
37 <tests>
38 <test>
39 <!-- test 1: check if identical outputs are produced with default parameters -->
40 <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" />
41 <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
42 <param name="rp2_pathways" value="1-rp2_metnet.csv" />
43 <param name="sink" value="2-sink.csv" />
44 <output_collection name="pathways" type="list">
45 <element name="rp_001_0001" ftype="xml" file="rp_001_0001.xml" sort="true"/>
46 <element name="rp_001_0006" ftype="xml" file="rp_001_0006.xml" sort="true"/>
47 <element name="rp_001_0011" ftype="xml" file="rp_001_0011.xml" sort="true"/>
48 <element name="rp_002_0001" ftype="xml" file="rp_002_0001.xml" sort="true"/>
49 <element name="rp_002_0011" ftype="xml" file="rp_002_0011.xml" sort="true"/>
50 <element name="rp_002_0021" ftype="xml" file="rp_002_0021.xml" sort="true"/>
51 <element name="rp_003_0001" ftype="xml" file="rp_003_0001.xml" sort="true"/>
52 <element name="rp_003_0131" ftype="xml" file="rp_003_0131.xml" sort="true"/>
53 <element name="rp_003_0261" ftype="xml" file="rp_003_0261.xml" sort="true"/>
54 </output_collection>
55 </test>
56 </tests>
57 <help><![CDATA[
58 rpCompletion
59 ============
60
61 Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data.
62
63 Input
64 -----
65
66 Required:
67
68 * **rp2_pathways**: (string) Path to the RetroPath2.0 pathways file
69 * **rp2_sink**: (string) Path to the rpextractsink file containing infos on molecules in the sink
70 * **rp2paths_compounds**: (string) Path to the rp2paths compounds file
71 * **rp2paths_pathways**: (string) Path to the rp2paths pathways file
72 * **outdir**: (string) Path to the output directory containing sbml completed pathways
73
74 Advanced options:
75
76 * **-upper_flux_bound**: (integer, default=9999) Upper flux bound value
77 * **-lower_flux_bound**: (integer, default=0) Lower flux bound value
78 * **-max_subpaths_filter**: (integer, default=10, 0=nofilter) Number of subpaths per path
79
80 Project Links
81 ---------------------
82 * `GitHub <https://github.com/brsynth/rptools>`_
83
84 Version
85 ----------
86
87 5.9.2
88
89 Authors
90 -------
91
92 * **Melchior du Lac**
93 * **Joan Hérisson**
94
95 Acknowledgments
96 ---------------
97
98 * Thomas Duigou
99
100 Licence
101 -------
102
103 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
104
105 ]]></help>
106 </tool>