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comparison get_sbml_model.xml @ 13:6bcd8f09158d draft default tip

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 8ab0b9452a029b409b18b80243958b4901bdeb3d
author tduigou
date Tue, 01 Apr 2025 10:00:36 +0000
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12:1aadcfdae10b 13:6bcd8f09158d
1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.3.0" profile="21.09" license="MIT"> 1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.4.0" 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="2.31">requests</requirement>
8 <requirement type="package" version="0.1.1">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 #import re 11 #import re
12 #if str($cond_src.from_src) == 'from_bigg' 12 #if str($cond_src.from_src) == 'from_bigg'
13 curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid.hostid}.xml.gz' | gunzip > '$model' && 13 curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid}.xml.gz' | gunzip > '$model' &&
14 #else 14 #else
15 #set model=$cond_src.input_file 15 #set model=$cond_src.input_file
16 #end if 16 #end if
17 python '$__tool_directory__/'get_infos.py 17 python '$__tool_directory__/'get_infos.py
18 '$model' 18 '$model'
19 --hostname-or-id '$cond_src.hostid.hostid' 19 #if str($cond_src.from_src) == 'from_bigg'
20 --taxid '$taxid' 20 --taxonid-outfile '$taxid_bigg'
21 --comp '$compartments' 21 --compartments-outfile '$compartments_bigg'
22 --biomass '$biomass' 22 --biomassid-outfile '$biomass_bigg'
23 #else
24 --biomassid '$cond_src.adv.biomassid'
25 --taxonid '$cond_src.adv.taxonid'
26 $cond_src.adv.standalone
27 --taxonid-outfile '$taxid_history'
28 --compartments-outfile '$compartments_history'
29 --biomassid-outfile '$biomass_history'
30 #end if
23 ]]></command> 31 ]]></command>
24 <inputs> 32 <inputs>
25 <conditional name="cond_src"> 33 <conditional name="cond_src">
26 <param name="from_src" type="select" label="Select source"> 34 <param name="from_src" type="select" label="Select source">
27 <option value="from_bigg" selected="True">Download model from BiGG</option> 35 <option value="from_bigg" selected="True">Download model from BiGG</option>
28 <option value="from_history">Select file from the History</option> 36 <option value="from_history">Select file from the History</option>
29 </param> 37 </param>
30 <when value="from_history"> 38 <when value="from_history">
31 <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/> 39 <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/>
32 <section name="hostid" title="Model's ID" expanded="false"> 40 <section name="adv" title="Advanced Options" expanded="false">
33 <param name="hostid" type="text" label="Model's hostname or ID" help="Model extended name or ID" optional="True"/> 41 <param name="biomassid" type="text" label="Biomass reaction ID" help="Biomass reaction ID" optional="True"/>
42 <param name="taxonid" type="text" label="Taxonomy ID" help="Taxonomy ID" optional="True"/>
43 <param argument="--standalone" type="boolean" truevalue="--standalone" falsevalue="" checked="false" label="Standalone mode" help="If true, do not retrieve taxonomy ID from Internet" />
34 </section> 44 </section>
35 </when> 45 </when>
36 <when value="from_bigg"> 46 <when value="from_bigg">
37 <section name="hostid" title="Model's ID" expanded="true"> 47 <param name="hostid" type="select" label="Strain">
38 <param name="hostid" type="select" label="Strain"> 48 <!-- Be careful, the text name is used for the hostname variable -->
39 <!-- Be careful, the text name is used for the hostname variable --> 49 <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option>
40 <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option> 50 <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option>
41 <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option> 51 <option value="iRC1080">Chlamydomonas reinhardtii (iRC1080)</option>
42 <option value="iRC1080">Chlamydomonas reinhardtii (iRC1080)</option> 52 <option value="iCN900">Clostridioides difficile 630 (iCN900)</option>
43 <option value="iCN900">Clostridioides difficile 630 (iCN900)</option> 53 <option value="iHN637">Clostridium ljungdahlii DSM 13528 (iHN637)</option>
44 <option value="iHN637">Clostridium ljungdahlii DSM 13528 (iHN637)</option> 54 <option value="iCHOv1_DG44">Cricetulus griseus (iCHOv1_DG44)</option>
45 <option value="iCHOv1_DG44">Cricetulus griseus (iCHOv1_DG44)</option> 55 <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option>
46 <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option> 56 <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option>
47 <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option> 57 <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option>
48 <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option> 58 <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option>
49 <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option> 59 <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option>
50 <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option> 60 <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option>
51 <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option> 61 <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option>
52 <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option> 62 <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option>
53 <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option> 63 <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option>
54 <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option> 64 <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option>
55 <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option> 65 <option value="Recon3D">Homo sapiens (Recon3D)</option>
56 <option value="Recon3D">Homo sapiens (Recon3D)</option> 66 <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option>
57 <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option> 67 <option value="RECON1">Homo sapiens (RECON1)</option>
58 <option value="RECON1">Homo sapiens (RECON1)</option> 68 <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option>
59 <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option> 69 <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option>
60 <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option> 70 <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option>
61 <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option> 71 <option value="iMM1415">Mus musculus (iMM1415)</option>
62 <option value="iMM1415">Mus musculus (iMM1415)</option> 72 <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option>
63 <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option> 73 <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option>
64 <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option> 74 <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option>
65 <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option> 75 <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option>
66 <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option> 76 <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option>
67 <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option> 77 <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option>
68 <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option> 78 <option value="iAM_Pk459">Plasmodium knowlesi strain H (iAM_Pk459)</option>
69 <option value="iAM_Pk459">Plasmodium knowlesi strain H (iAM_Pk459)</option> 79 <option value="iAM_Pv461">Plasmodium vivax Sal-1 (iAM_Pv461)</option>
70 <option value="iAM_Pv461">Plasmodium vivax Sal-1 (iAM_Pv461)</option> 80 <option value="iJN746">Pseudomonas putida KT2440 (iJN746)</option>
71 <option value="iJN746">Pseudomonas putida KT2440 (iJN746)</option> 81 <option value="iJN1463">Pseudomonas putida KT2440 (iJN1463)</option>
72 <option value="iJN1463">Pseudomonas putida KT2440 (iJN1463)</option> 82 <option value="iND750">Saccharomyces cerevisiae S288C (iND750)</option>
73 <option value="iND750">Saccharomyces cerevisiae S288C (iND750)</option> 83 <option value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option>
74 <option value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option> 84 <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option>
75 <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option> 85 <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option>
76 <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option> 86 <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option>
77 <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option> 87 <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option>
78 <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option> 88 <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option>
79 <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option> 89 <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option>
80 <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option> 90 <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option>
81 <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option> 91 <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option>
82 <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option> 92 <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option>
83 <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option> 93 <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option>
84 <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option> 94 <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option>
85 <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option> 95 <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option>
86 <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option> 96 </param>
87 </param>
88 </section>
89 </when> 97 </when>
90 </conditional> 98 </conditional>
91 </inputs> 99 </inputs>
92 <outputs> 100 <outputs>
93 <data name="model" format="sbml" label="${cond_src.hostid.hostid}"> 101 <data name="model" format="sbml" label="${cond_src.hostid}">
94 <filter>cond_src['from_src'] == 'from_bigg'</filter> 102 <filter>cond_src['from_src'] == 'from_bigg'</filter>
95 </data> 103 </data>
96 <data name="taxid" format="tsv" label="${cond_src.hostid.hostid} (taxon id)" /> 104 <data name="taxid_bigg" format="tsv" label="${cond_src.hostid} (taxon id)">
97 <data name="compartments" format="tsv" label="${cond_src.hostid.hostid} (compartments)" /> 105 <filter>cond_src['from_src'] == 'from_bigg'</filter>
98 <data name="biomass" format="tsv" label="${cond_src.hostid.hostid} (biomass reactions)" /> 106 </data>
107 <data name="compartments_bigg" format="tsv" label="${cond_src.hostid} (compartments)">
108 <filter>cond_src['from_src'] == 'from_bigg'</filter>
109 </data>
110 <data name="biomass_bigg" format="tsv" label="${cond_src.hostid} (biomass reactions)">
111 <filter>cond_src['from_src'] == 'from_bigg'</filter>
112 </data>
113 <data name="taxid_history" format="tsv" label="${cond_src.input_file.name} (taxon id)">
114 <filter>cond_src['from_src'] == 'from_history'</filter>
115 </data>
116 <data name="compartments_history" format="tsv" label="${cond_src.input_file.name} (compartments)">
117 <filter>cond_src['from_src'] == 'from_history'</filter>
118 </data>
119 <data name="biomass_history" format="tsv" label="${cond_src.input_file.name} (biomass reactions)">
120 <filter>cond_src['from_src'] == 'from_history'</filter>
121 </data>
99 </outputs> 122 </outputs>
100 <tests> 123 <tests>
101 <test expect_num_outputs="4"> 124 <test expect_num_outputs="4">
102 <conditional name="cond_src"> 125 <conditional name="cond_src">
103 <param name="from_src" value="from_bigg" /> 126 <param name="from_src" value="from_bigg" />
104 <section name="hostid"> 127 <param name="hostid" value="iML1515" />
105 <param name="hostid" value="iML1515" />
106 </section>
107 </conditional> 128 </conditional>
108 <output name="model" md5="9bf81d20cab5476700697ded95b716d1" /> 129 <output name="model" md5="9bf81d20cab5476700697ded95b716d1" />
109 <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" /> 130 <output name="taxid_bigg" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
110 <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" /> 131 <output name="compartments_bigg" md5="e93a875a2d8efc10a880ae3ac0018236" />
111 <output name="biomass" md5="95c0255bd5dd8753c6dde53c0f2958ea" /> 132 <output name="biomass_bigg" md5="95c0255bd5dd8753c6dde53c0f2958ea" />
112 </test> 133 </test>
113 <test expect_num_outputs="3"> 134 <test expect_num_outputs="3">
114 <conditional name="cond_src"> 135 <conditional name="cond_src">
115 <param name="from_src" value="from_history" /> 136 <param name="from_src" value="from_history" />
116 <section name="hostid"> 137 <param name="input_file" value="e_coli_core.xml" />
117 <param name="hostid" value="Escherichia coli str. K-12 substr. MG1655" /> 138 </conditional>
118 </section> 139 <output name="taxid_history" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
119 <param name="input_file" value="e_coli_core.xml" /> 140 <output name="compartments_history" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
120 </conditional> 141 <output name="biomass_history" md5="d10baa335181450c7bffa9b4ca01754a" />
121 <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" /> 142 </test>
122 <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" /> 143 <test expect_num_outputs="3">
123 <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" /> 144 <conditional name="cond_src">
124 </test> 145 <param name="from_src" value="from_history" />
125 <test expect_num_outputs="3"> 146 <param name="input_file" value="e_coli_core.xml" />
126 <conditional name="cond_src"> 147 <section name="adv">
127 <param name="from_src" value="from_history" /> 148 <param name="standalone" value="true" />
128 <section name="hostid"> 149 </section>
129 <param name="hostid" value="e_coli_core" /> 150 </conditional>
130 </section> 151 <output name="taxid_history" md5="b4f2c5588318a1043520ef77c1db9865" />
131 <param name="input_file" value="e_coli_core.xml" /> 152 <output name="compartments_history" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
132 </conditional> 153 <output name="biomass_history" md5="d10baa335181450c7bffa9b4ca01754a" />
133 <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" /> 154 </test>
134 <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" /> 155 <test expect_num_outputs="3">
135 <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" /> 156 <conditional name="cond_src">
136 </test> 157 <param name="from_src" value="from_history" />
137 <test expect_num_outputs="3"> 158 <param name="input_file" value="e_coli_core.xml" />
138 <conditional name="cond_src"> 159 <section name="adv">
139 <param name="from_src" value="from_history" /> 160 <param name="taxonid" value="511145" />
140 <section name="hostid"> 161 </section>
141 <param name="hostid" value="iMM1415" /> 162 </conditional>
142 </section> 163 <output name="taxid_history" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
143 <param name="input_file" value="e_coli_core.xml" /> 164 <output name="compartments_history" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
144 </conditional> 165 <output name="biomass_history" md5="d10baa335181450c7bffa9b4ca01754a" />
145 <output name="taxid" md5="9c5ebe6ee91a632cbfb244435db7ce7e" /> 166 </test>
146 <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" /> 167 <test expect_num_outputs="3">
147 <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" /> 168 <conditional name="cond_src">
169 <param name="from_src" value="from_history" />
170 <param name="input_file" value="e_coli_core.xml" />
171 <section name="adv">
172 <param name="taxonid" value="83333" />
173 </section>
174 </conditional>
175 <output name="taxid_history" md5="ec29688652dd49becf7be2a6c2469287" />
176 <output name="compartments_history" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
177 <output name="biomass_history" md5="d10baa335181450c7bffa9b4ca01754a" />
178 </test>
179 <test expect_num_outputs="3">
180 <conditional name="cond_src">
181 <param name="from_src" value="from_history" />
182 <param name="input_file" value="iMS570_cobra_without_constraints.xml" />
183 </conditional>
184 <output name="taxid_history" md5="b4f2c5588318a1043520ef77c1db9865" />
185 <output name="compartments_history" md5="973d345179c06304590bf27c7774db51" />
186 <output name="biomass_history" md5="08fa413cfe0ff6439378a63395f49c0f" />
187 </test>
188 <test expect_num_outputs="3">
189 <conditional name="cond_src">
190 <param name="from_src" value="from_history" />
191 <param name="input_file" value="iMS570_cobra_without_constraints.xml" />
192 <section name="adv">
193 <param name="taxonid" value="e_coli_core" />
194 </section>
195 </conditional>
196 <output name="taxid_history" md5="cfc5df6325c0f6a519eded6ee975a0c3" />
197 <output name="compartments_history" md5="973d345179c06304590bf27c7774db51" />
198 <output name="biomass_history" md5="08fa413cfe0ff6439378a63395f49c0f" />
148 </test> 199 </test>
149 </tests> 200 </tests>
150 <help><![CDATA[ 201 <help><![CDATA[
151 Pick SBML Model 202 Pick SBML Model
152 ================= 203 =================