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comparison selenzy_wrapper.xml @ 3:be121e7d0c9d draft default tip

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planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 45a7c182f39c67507b05e39509b865a04ecdd1f9
author tduigou
date Tue, 23 May 2023 14:17:15 +0000
parents 164ccfcd18ec
children
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2:164ccfcd18ec 3:be121e7d0c9d
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 python -m selenzy_wrapper '$pathway' '$uniprot_ids' 11 python -m selenzy_wrapper '$pathway' '$uniprot_ids'
12 --nb_targets '$adv.nb_targets' 12 --nb_targets '$adv.nb_targets'
13 --d '$adv.direction' 13 --d '$adv.direction'
14 $adv.NoMSA 14 $adv.NoMSA
15 --host_taxID '$adv.host_taxID' 15 #if str($host_taxID_type_conditional.host_taxID_type) == "tsv":
16 --host_taxID `sed 1d ${host_taxID_type_conditional.host_taxID_file}`
17 #else:
18 --host_taxID '$host_taxID_type_conditional.host_taxID_int'
19 #end if
16 #if str($adv.enzyme_taxIDs) != "": 20 #if str($adv.enzyme_taxIDs) != "":
17 --enzyme_taxIDs '$adv.enzyme_taxIDs' 21 --enzyme_taxIDs '$adv.enzyme_taxIDs'
18 #end if 22 #end if
19 --nb_ids '$adv.nb_ids' 23 --nb_ids '$adv.nb_ids'
20 --to_csv '$uniprot_ids_csv' 24 --to_csv '$uniprot_ids_csv'
21 --data-path "\${TMPDIR:-.}" 25 --data-path "\${TMPDIR:-.}"
22 ]]></command> 26 ]]></command>
23 <inputs> 27 <inputs>
24 <param name="pathway" type="data" format="sbml" label="Pathway (SBML)" /> 28 <param name="pathway" type="data" format="sbml" label="Pathway (SBML)" />
29 <conditional name="host_taxID_type_conditional">
30 <param name="host_taxID_type" type="select" label="Host taxon ID type">
31 <option value="integer" selected="True">Value</option>
32 <option value="tsv">File</option>
33 </param>
34 <when value="integer">
35 <param name="host_taxID_int" type="integer" label="Host taxon ID value" value="83333" help="default: 83333 [E. coli K12]" />
36 </when>
37 <when value="tsv">
38 <param name="host_taxID_file" type="data" format="tsv" label="Host taxon ID file" />
39 </when>
40 </conditional>
25 <section name="adv" title="Advanced Options" expanded="false"> 41 <section name="adv" title="Advanced Options" expanded="false">
26 <param name="host_taxID" type="integer" value="83333" label="Host taxon ID" help="Taxon ID of the chassis (default: 83333 [E. coli K12])" />
27 <param name="enzyme_taxIDs" type="text" value="" label="Comma separated taxon IDs of output enzyme sequences" /> 42 <param name="enzyme_taxIDs" type="text" value="" label="Comma separated taxon IDs of output enzyme sequences" />
28 <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" help=" Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]" /> 43 <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" help=" Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]" />
29 <param name="nb_targets" type="integer" value="500" min="1" label="Number of targets to display in results" help="Number of targets to display in results (before taxon IDs filtering) [default = 500]" /> 44 <param name="nb_targets" type="integer" value="500" min="1" label="Number of targets to display in results" help="Number of targets to display in results (before taxon IDs filtering) [default = 500]" />
30 <param name="direction" type="float" value="0" label="Use similarity values for preferred reaction direction only" help="You can choose to rank similarities in both reaction directions or to use only the direction of the reaction based on a consensus list that has been generated according to reaction information based on curated information from MetaCyc (Metabolic Pathway Database) [default=0 (OFF)]" /> 45 <param name="direction" type="float" value="0" label="Use similarity values for preferred reaction direction only" help="You can choose to rank similarities in both reaction directions or to use only the direction of the reaction based on a consensus list that has been generated according to reaction information based on curated information from MetaCyc (Metabolic Pathway Database) [default=0 (OFF)]" />
31 <param argument="--NoMSA" type="boolean" falsevalue="--NoMSA" truevalue="" checked="true" display="checkboxes" label="Do not compute MSA/conservation scores ?" help="Do not compute Multiple Sequence Alignment and conservation scores ? (MSA scores are computed by default)" /> 46 <param argument="--NoMSA" type="boolean" falsevalue="--NoMSA" truevalue="" checked="true" display="checkboxes" label="Do not compute MSA/conservation scores ?" help="Do not compute Multiple Sequence Alignment and conservation scores ? (MSA scores are computed by default)" />