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comparison selenzy.xml @ 1:34a9d136a5bf draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Tue, 08 Feb 2022 11:12:28 +0000
parents 481f7c35323d
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0:481f7c35323d 1:34a9d136a5bf
1 <tool id="selenzy-wrapper" name="Selenzyme" version="0.1.0"> 1 <tool id="selenzy-wrapper" name="Selenzyme" version="@TOOL_VERSION@" profile="19.09">
2 <description>Performs enzyme selection from a reaction query</description> 2 <description>Performs enzyme selection from a reaction query</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.1.0">selenzy_wrapper</requirement> 4 <token name="@TOOL_VERSION@">0.2.0</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">selenzy_wrapper</requirement>
5 </requirements> 8 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
7 python -m selenzy_wrapper '$pathway' '$uniprot_ids' 10 python -m selenzy_wrapper '$pathway' '$uniprot_ids'
8 --nb_targets '$adv.nb_targets' 11 --nb_targets '$adv.nb_targets'
9 --d '$adv.direction' 12 --d '$adv.direction'
10 #if str($adv.NoMSA) == "false": 13 #if str($adv.NoMSA) == "false":
11 --NoMSA 14 --NoMSA
12 #end if 15 #end if
13 --taxonIDs '$adv.taxonIDs' 16 --host_taxID '$adv.host_taxID'
17 #if str($adv.enzyme_taxIDs) != "":
18 --enzyme_taxIDs '$adv.enzyme_taxIDs'
19 #end if
14 --nb_ids '$adv.nb_ids' 20 --nb_ids '$adv.nb_ids'
15 --to_csv '$uniprot_ids_csv' 21 --to_csv '$uniprot_ids_csv'
16 ]]></command> 22 ]]></command>
17 <inputs> 23 <inputs>
18 <param name="pathway" type="data" format="xml" label="Pathway (SBML)" /> 24 <param name="pathway" type="data" format="xml" label="Pathway (SBML)" />
19 <section name="adv" title="Advanced Options" expanded="false"> 25 <section name="adv" title="Advanced Options" expanded="false">
20 <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" /> 26 <param name="host_taxID" type="integer" value="83333" label="Host taxon ID" />
21 <param name="nb_targets" type="integer" value="500" label="Number of targets to display in results" /> 27 <param name="enzyme_taxIDs" type="text" value="" label="Comma separated taxon IDs of output enzyme sequences" />
22 <param name="direction" type="float" value="0" label="Use similiarity values for preferred reaction direction only" /> 28 <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" />
23 <param name="NoMSA" type="boolean" label="Do not compute MSA/conservation scores ?" checked="true" display="checkboxes" /> 29 <param name="nb_targets" type="integer" value="500" label="Number of targets to display in results" />
24 <param name="taxonIDs" type="text" label="Comma separated taxon ids (first considered as the host)" value="83333" /> 30 <param name="direction" type="float" value="0" label="Use similiarity values for preferred reaction direction only" />
31 <param name="NoMSA" type="boolean" checked="true" display="checkboxes" label="Do not compute MSA/conservation scores ?" />
25 </section> 32 </section>
26 </inputs> 33 </inputs>
27 <outputs> 34 <outputs>
28 <data name="uniprot_ids" format="xml" label="Uniprot IDs" /> 35 <data name="uniprot_ids" format="xml" label="Uniprot IDs" />
29 <data name="uniprot_ids_csv" format="csv" label="Uniprot IDs" /> 36 <data name="uniprot_ids_csv" format="csv" label="Uniprot IDs" />
48 * **pathway_file**\ : (string) path to pathway file 55 * **pathway_file**\ : (string) path to pathway file
49 * **nb_targets**\ : (integer) Number of targets to display in results (before taxon IDs filtering) [default = 20] 56 * **nb_targets**\ : (integer) Number of targets to display in results (before taxon IDs filtering) [default = 20]
50 * **nb_ids**\ : (integer) Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)] 57 * **nb_ids**\ : (integer) Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]
51 * **direction**\ : (float) Use similiarity values for preferred reaction direction only [default=0 (OFF)] 58 * **direction**\ : (float) Use similiarity values for preferred reaction direction only [default=0 (OFF)]
52 * **NoMSA**\ : (boolean) Do not compute MSA/conservation scores 59 * **NoMSA**\ : (boolean) Do not compute MSA/conservation scores
53 * **taxonIDs**\ : (string) Comma separated taxon ids [default: 83333 (E. coli K12)]. The first taxon ID is the one of the chassis, following ones are taxon IDs of output enzyme sequences 60 * **host_taxID**\ : (string) Taxon ID of the chassis (default: 83333 [E. coli K12])
61 * **enzyme_taxIDs**\ : (string) Comma separated taxon IDs of output enzyme sequences
54 62
55 Output 63 Output
56 ------ 64 ------
57 65
58 * **outfile**\ : (string) Path to output file 66 * **outfile**\ : (string) Path to output file
63 * `GitHub <https://github.com/brsynth/selenzy-wrapper>`_ 71 * `GitHub <https://github.com/brsynth/selenzy-wrapper>`_
64 72
65 Version 73 Version
66 ---------- 74 ----------
67 75
68 0.1.0 76 0.2.0
69 77
70 Authors 78 Authors
71 ------- 79 -------
72 * **Joan Hérisson** 80 * **Joan Hérisson**
73 81
81 89
82 * Thomas Duigou 90 * Thomas Duigou
83 91
84 ]]></help> 92 ]]></help>
85 <citations> 93 <citations>
86 <citation type="bibtex"> 94 <citation type="doi">10.1093/bioinformatics/bty065</citation>
87 @article{10.1093/bioinformatics/bty065,
88 title={Selenzyme: enzyme selection tool for pathway design},
89 author={Pablo Carbonell, Jerry Wong, Neil Swainston, Eriko Takano, Nicholas J Turner, Nigel S Scrutton, Douglas B Kell, Rainer Breitling, Jean-Loup Faulon},
90 volume={34},
91 pages={2153–2154},
92 year={2018},
93 doi = {10.1093/bioinformatics/bty065},
94 url = {https://doi.org/10.1093/bioinformatics/bty065},
95 }
96 </citation>
97 </citations> 95 </citations>
98 </tool> 96 </tool>