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comparison get_sbml_model.xml @ 7:33be348bf9d6 draft

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
author tduigou
date Tue, 26 Sep 2023 12:59:14 +0000
parents 07640c01f56c
children 06366f104f78
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6:07640c01f56c 7:33be348bf9d6
1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.0.4" profile="21.09" license="MIT"> 1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.1.0" 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 </requirements> 9 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
10 #if str($cond_src.from_src) == 'from_bigg' 11 #if str($cond_src.from_src) == 'from_bigg'
11 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' &&
12 #else 13 #else
13 cp '${cond_src.input_file}' '$model' && 14 python -m taxonid '${cond_src.hostname}' --output-file tmpfile &&
15 echo "#ID" > '$taxid' &&
16 cat tmpfile >> '$taxid' &&
14 #end if 17 #end if
18 echo "listdir:";
19 ls;
15 python '$__tool_directory__/'get_infos.py 20 python '$__tool_directory__/'get_infos.py
16 '$model' 21 #if str($cond_src.from_src) == 'from_bigg'
17 --hostid '${cond_src.hostid}' 22 '$model'
18 --comp '$compartments' 23 --taxid '$taxid'
19 --biomass '$biomass' 24 #else
20 --taxid '$taxid' 25 '${cond_src.input_file}'
26 #end if
27 --hostid '${cond_src.hostid}'
28 --comp '$compartments'
29 --biomass '$biomass'
21 ]]></command> 30 ]]></command>
22 <inputs> 31 <inputs>
23 <conditional name="cond_src"> 32 <conditional name="cond_src">
24 <param name="from_src" type="select" label="Select source"> 33 <param name="from_src" type="select" label="Select source">
25 <option value="from_bigg" selected="True">Download model from BiGG</option> 34 <option value="from_bigg" selected="True">Download model from BiGG</option>
26 <option value="from_history">Select file from the History</option> 35 <option value="from_history">Select file from the History</option>
27 </param> 36 </param>
28 <when value="from_history"> 37 <when value="from_history">
38 <param name="hostname" type="text" help="Fullname of the model">
39 <validator type="empty_field" message="The fullname of the organism is required"/>
40 </param>
29 <param name="hostid" type="text" help="ID of the model"> 41 <param name="hostid" type="text" help="ID of the model">
30 <validator type="empty_field" message="An ID is required"/> 42 <validator type="empty_field" message="ID of the organism is required"/>
31 </param> 43 </param>
32 <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/> 44 <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/>
33 </when> 45 </when>
34 <when value="from_bigg"> 46 <when value="from_bigg">
35 <param name="hostid" type="select" label="Strain"> 47 <param name="hostid" type="select" label="Strain">
83 </param> 95 </param>
84 </when> 96 </when>
85 </conditional> 97 </conditional>
86 </inputs> 98 </inputs>
87 <outputs> 99 <outputs>
88 <data name="model" format="sbml" label="${cond_src.hostid}" /> 100 <data name="model" format="sbml" label="${cond_src.hostid}">
101 <filter>cond_src['from_src'] == 'from_bigg'</filter>
102 </data>
89 <data name="taxid" format="tsv" label="${cond_src.hostid} (taxon id)" /> 103 <data name="taxid" format="tsv" label="${cond_src.hostid} (taxon id)" />
90 <data name="compartments" format="tsv" label="${cond_src.hostid} (compartments)" /> 104 <data name="compartments" format="tsv" label="${cond_src.hostid} (compartments)" />
91 <data name="biomass" format="tsv" label="${cond_src.hostid} (biomass reactions)" /> 105 <data name="biomass" format="tsv" label="${cond_src.hostid} (biomass reactions)" />
92 </outputs> 106 </outputs>
93 <tests> 107 <tests>
94 <test> 108 <test>
95 <conditional name="cond_src"> 109 <param name="from_src" value="from_bigg" />
96 <param name="from_src" value="from_bigg" /> 110 <param name="hostid" value="iML1515" />
97 <param name="hostid" value="iML1515" />
98 </conditional>
99 <output name="model" md5="9bf81d20cab5476700697ded95b716d1" /> 111 <output name="model" md5="9bf81d20cab5476700697ded95b716d1" />
100 <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" /> 112 <output name="taxid" md5="7c62bd818057838b3557c8d87cca47fc" />
101 <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" /> 113 <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" />
102 <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06" /> 114 <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06" />
103 </test> 115 </test>
104 <test> 116 <test>
105 <conditional name="cond_src"> 117 <conditional name="cond_src">
106 <param name="from_src" value="from_history" /> 118 <param name="from_src" value="from_history" />
119 <param name="hostname" value="Escherichia coli str. K-12 substr. MG1655" />
107 <param name="hostid" value="e_coli_core" /> 120 <param name="hostid" value="e_coli_core" />
108 <param name="input_file" value="e_coli_core.xml" /> 121 <param name="input_file" value="e_coli_core.xml" />
109 </conditional> 122 </conditional>
110 <output name="model" md5="4574760460afe9e1b3388dc15f354706" /> 123 <output name="taxid" md5="ee08b511771328e6254775a51779d421" />
111 <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
112 <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" /> 124 <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
113 <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" /> 125 <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" />
114 </test> 126 </test>
115 </tests> 127 </tests>
116 <help><![CDATA[ 128 <help><![CDATA[