Mercurial > repos > tduigou > get_sbml_model

comparison get_sbml_model.xml @ 9:6a2871e89352 draft default tip

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 537d7fefe58984b8f7ca66010153a2fdc35ddf4b
author tduigou
date Wed, 14 Feb 2024 15:25:38 +0000
parents 768ed7cc0978
children
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8:768ed7cc0978 9:6a2871e89352
1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.1.0" profile="21.09" license="MIT"> 1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.2.0" profile="21.09" license="MIT">
2 <description>Get an SBML model (BiGG)</description> 2 <description>Get an SBML model (BiGG)</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="7.81.0">curl</requirement> 4 <requirement type="package" version="7.81.0">curl</requirement>
5 <requirement type="package" version="1.11">gzip</requirement> 5 <requirement type="package" version="1.11">gzip</requirement>
6 <requirement type="package" version="5.19.2">python-libsbml</requirement> 6 <requirement type="package" version="5.19.2">python-libsbml</requirement>
7 <requirement type="package" version="2.29">requests</requirement> 7 <requirement type="package" version="2.29">requests</requirement>
8 <requirement type="package" version="0.1.0">taxonid</requirement> 8 <requirement type="package" version="0.1.1">taxonid</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #if str($cond_src.from_src) == 'from_bigg' 11 #if str($cond_src.from_src) == 'from_bigg'
12 curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid}.xml.gz' | gunzip > '$model' && 12 curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid}.xml.gz' | gunzip > '$model' &&
13 #else
14 python -m taxonid '${cond_src.hostname}' --output-file tmpfile &&
15 echo "#ID" > '$taxid' &&
16 cat tmpfile >> '$taxid' &&
17 #end if 13 #end if
18 echo "listdir:";
19 ls;
20 python '$__tool_directory__/'get_infos.py 14 python '$__tool_directory__/'get_infos.py
21 #if str($cond_src.from_src) == 'from_bigg' 15 #if str($cond_src.from_src) == 'from_bigg'
22 '$model' 16 '$model'
23 --bigg 17 --bigg
24 --taxid '$taxid'
25 #else 18 #else
26 '${cond_src.input_file}' 19 '${cond_src.input_file}'
27 #end if 20 #end if
28 --hostid '${cond_src.hostid}' 21 --hostname '${cond_src.hostid}'
22 --taxid '$taxid'
29 --comp '$compartments' 23 --comp '$compartments'
30 --biomass '$biomass' 24 --biomass '$biomass'
31 ]]></command> 25 ]]></command>
32 <inputs> 26 <inputs>
33 <conditional name="cond_src"> 27 <conditional name="cond_src">
34 <param name="from_src" type="select" label="Select source"> 28 <param name="from_src" type="select" label="Select source">
35 <option value="from_bigg" selected="True">Download model from BiGG</option> 29 <option value="from_bigg" selected="True">Download model from BiGG</option>
36 <option value="from_history">Select file from the History</option> 30 <option value="from_history">Select file from the History</option>
37 </param> 31 </param>
38 <when value="from_history"> 32 <when value="from_history">
39 <param name="hostname" type="text" help="Fullname of the model"> 33 <param name="hostid" type="text" label="Model's fullname" help="Model extended name">
40 <validator type="empty_field" message="The fullname of the organism is required"/> 34 <validator type="empty_field" message="Organism extended name required"/>
41 </param>
42 <param name="hostid" type="text" help="ID of the model">
43 <validator type="empty_field" message="ID of the organism is required"/>
44 </param> 35 </param>
45 <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/> 36 <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/>
46 </when> 37 </when>
47 <when value="from_bigg"> 38 <when value="from_bigg">
48 <param name="hostid" type="select" label="Strain"> 39 <param name="hostid" type="select" label="Strain">