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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit c1b249f25f3143e21980cd7daecb1aebb88ef948-dirty
author tduigou
date Fri, 24 Oct 2025 08:37:01 +0000
parents 874093da8436
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0:874093da8436 1:c33bde07cbc7
1 <tool id="rptools_rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 1 <tool id="rptools_rpcompletion" name="Complete Reactions"
2 <description>Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors</description> 2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
3 <description>Completes mono-component reactions output by RetroPath2.0 with the appropriate
4 cofactors</description>
3 <macros> 5 <macros>
4 <import>macros.xml</import> 6 <import>macros.xml</import>
5 </macros> 7 </macros>
6 <expand macro="requirements"/> 8 <expand macro="requirements" />
7 <stdio> 9 <stdio>
8 <exit_code range="1" level="fatal" description="Could not Xref compartment_id" /> 10 <exit_code range="1" level="fatal" description="Could not Xref compartment_id" />
9 <exit_code range="2" level="fatal" description="ValueError returned" /> 11 <exit_code range="2" level="fatal" description="ValueError returned" />
12 <regex match="Continuing without sink molecule" source="both" level="warning"
13 description="The sink file is empty or not found" />
10 </stdio> 14 </stdio>
11 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
16 TMPDIR="\${TMPDIR:-.}/rr_cache" &&
17 mkdir -p "\${TMPDIR}" &&
18 #if str($sink.cond) == 'empty'
19 echo '"Name","InChI"' > empty_sink.csv &&
20 #set sinkfile='empty_sink.csv'
21 #else
22 #set sinkfile=$sink.sinkfile
23 #end if
24
12 python -m rptools.rpcompletion 25 python -m rptools.rpcompletion
13 '$rp2_pathways' 26 '$rp2_pathways'
14 '$sink' 27 $sinkfile
15 '$rp2paths_compounds' 28 '$rp2paths_compounds'
16 '$rp2paths_pathways' 29 '$rp2paths_pathways'
17 completed_pathways 30 completed_pathways
18 --upper_flux_bound '$adv.upper_flux_bound' 31 --upper_flux_bound '$adv.upper_flux_bound'
19 --lower_flux_bound '$adv.lower_flux_bound' 32 --lower_flux_bound '$adv.lower_flux_bound'
20 --max_subpaths_filter '$adv.max_subpaths_filter' 33 --max_subpaths_filter '$adv.max_subpaths_filter'
21 --cache-dir "\${TMPDIR:-.}" 34 --chemical-space '$adv.chemical_space'
35 #if $adv.cofile
36 --cofactors '$adv.cofile'
37 #end if
38 #if not $sink.error_codes
39 --silent
40 #end if
41 --cache-dir "\${TMPDIR:-.}"
22 ]]></command> 42 ]]></command>
23 <inputs> 43 <inputs>
24 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" /> 44 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
25 <param name="rp2paths_compounds" type="data" format="tabular" label="RP2paths compounds" /> 45 <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" /> 46 <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" /> 47 <conditional name="sink">
48 <param name="cond" type="select" label="Empty sink">
49 <option value="provided" selected="True">Provided</option>
50 <option value="empty">Empty</option>
51 </param>
52 <when value="provided">
53 <param name="sinkfile" type="data" format="csv" label="Sink File"
54 help="Sink file which comprises all compounds that are considered as granted in your system." />
55 <param name="error_codes" type="boolean" checked="true"
56 label="Return error codes" />
57 </when>
58 <when value="empty">
59 <param name="error_codes" type="boolean" checked="false"
60 label="Return error codes" />
61 </when>
62 </conditional>
28 <section name="adv" title="Advanced Options" expanded="false"> 63 <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." /> 64 <param argument="max_subpaths_filter" type="integer" value="10" min="0"
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." /> 65 label="Max subpaths generated per pathway"
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." /> 66 help="Maximal number of subpaths to be created per master pathway." />
67 <param argument="upper_flux_bound" type="integer" value="10000" min="-10000" max="10000"
68 label="Upper flux bound"
69 help="Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
70 <param argument="lower_flux_bound" type="integer" value="-10000" min="-10000"
71 max="10000" label="Lower flux bound"
72 help="Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
73 <param name="chemical_space" type="select" label="Chemical space">
74 <option value="mnx4.4" selected="True">mnx4.4</option>
75 <option value="mnx3.1">mnx3.1</option>
76 </param>
77 <param name="cofile" type="data" format="txt,tsv,tabular" optional="True"
78 label="Cofactor file" />
32 </section> 79 </section>
33 </inputs> 80 </inputs>
34 <outputs> 81 <outputs>
35 <collection name="pathways" type="list" label="${tool.name}"> 82 <collection name="pathways" type="list" label="${tool.name}">
36 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml" format="xml" directory="completed_pathways" visible="false" /> 83 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml" format="xml"
84 directory="completed_pathways" visible="false" />
37 </collection> 85 </collection>
38 </outputs> 86 </outputs>
39 <tests> 87 <tests>
40 <test> 88 <test>
41 <!-- test 1: check if outputs are represented in an expected number --> 89 <!-- test 1: check if outputs are represented in an expected number -->
42 <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" /> 90 <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" />
43 <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" /> 91 <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
44 <param name="rp2_pathways" value="1-rp2_metnet.csv" /> 92 <param name="rp2_pathways" value="1-rp2_metnet.csv" />
45 <param name="sink" value="2-sink.csv" /> 93 <conditional name="sink">
46 <output_collection name="pathways" type="list" count="9"/> 94 <param name="cond" value="provided" />
95 <param name="sinkfile" value="2-sink.csv" />
96 </conditional>
97 <output_collection name="pathways" type="list" count="10" />
47 </test> 98 </test>
48 </tests> 99 </tests>
49 <help><![CDATA[ 100 <help><![CDATA[
50 rpCompletion 101 rpCompletion
51 ============ 102 ============
52 103
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. 104 Completes mono-component reactions output by `RetroPath2.0 <https://www.doi.org/10.1016/j.ymben.2017.12.002>`_ 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.
70 105
71 Output 106 Output
72 ------ 107 ------
73 108
74 * **pathways**: SBML completed pathways 109 * **pathways**: SBML completed pathways
75 ]]></help> 110 ]]></help>
76 <expand macro="creator"/> 111 <expand macro="creator" />
77 <citations> 112 <citations>
78 <citation type="doi">10.1038/s41467-022-32661-x</citation> 113 <citation type="doi">10.1038/s41467-022-32661-x</citation>
79 </citations> 114 </citations>
80 </tool> 115 </tool>