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comparison rpcompletion.xml @ 0:ae16d7ce27d1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
author tduigou
date Tue, 28 Mar 2023 12:08:32 +0000
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1 <tool id="rptools_rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <stdio>
8 <exit_code range="1" level="fatal" description="Could not Xref compartment_id" />
9 <exit_code range="2" level="fatal" description="ValueError returned" />
10 </stdio>
11 <command detect_errors="exit_code"><![CDATA[
12 python -m rptools.rpcompletion
13 '$rp2_pathways'
14 '$sink'
15 '$rp2paths_compounds'
16 '$rp2paths_pathways'
17 completed_pathways
18 --upper_flux_bound '$adv.upper_flux_bound'
19 --lower_flux_bound '$adv.lower_flux_bound'
20 --max_subpaths_filter '$adv.max_subpaths_filter'
21 --cache-dir "\${TMPDIR:-.}"
22 ]]></command>
23 <inputs>
24 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
25 <param name="rp2paths_compounds" type="data" format="tabular" label="RP2paths compounds" />
26 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
27 <param name="sink" type="data" format="csv" label="Sink from SBML" />
28 <section name="adv" title="Advanced Options" expanded="false">
29 <param argument="max_subpaths_filter" type="integer" value="10" min="1" max="1000" label="Max subpaths generated per pathway" help="Maximal number of subpaths to be created per master pathway." />
30 <param argument="upper_flux_bound" type="integer" value="10000" min="-10000" max="10000" label="Upper flux bound" help="Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
31 <param argument="lower_flux_bound" type="integer" value="-10000" min="-10000" max="10000" label="Lower flux bound" help="Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
32 </section>
33 </inputs>
34 <outputs>
35 <collection name="pathways" type="list" label="${tool.name}">
36 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml" format="xml" directory="completed_pathways" visible="false" />
37 </collection>
38 </outputs>
39 <tests>
40 <test>
41 <!-- test 1: check if outputs are represented in an expected number -->
42 <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" />
43 <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
44 <param name="rp2_pathways" value="1-rp2_metnet.csv" />
45 <param name="sink" value="2-sink.csv" />
46 <output_collection name="pathways" type="list" count="9"/>
47 </test>
48 </tests>
49 <help><![CDATA[
50 rpCompletion
51 ============
52
53 Completes mono-component reactions output by `RetroPath2.0 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ 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.
54
55 Input
56 -----
57
58 Required:
59
60 * **RetroPath2.0 metabolic network**: RetroPath2.0 pathways file
61 * **Sink from SBML**: rpextractsink file containing infos on molecules in the sink
62 * **RP2paths compounds**: rp2paths compounds file
63 * **RP2paths pathways**: rp2paths pathways file
64
65 Advanced options:
66
67 * **Upper flux bound**: (integer, default=9999) Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created.
68 * **Lower flux bound**: (integer, default=0) Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created.
69 * **Max subpaths generated per pathway**: (integer, default=10, 0=nofilter) Maximal number of subpaths to be created per master pathway.
70
71 Output
72 ------
73
74 * **pathways**: SBML completed pathways
75 ]]></help>
76 <expand macro="creator"/>
77 <citations>
78 <citation type="doi">10.1038/s41467-022-32661-x</citation>
79 </citations>
80 </tool>