Mercurial > repos > iuc > straindesign_analyzing_model

comparison analyzing-model.xml @ 0:490a37e24bed draft

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planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
author iuc
date Sun, 02 Oct 2022 19:27:06 +0000
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children 3b09226992ff
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1 <tool id="straindesign_analyzing_model" name="StrainDesign analyzing-model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
2 <description>Produce a pareto plot for a biological model</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ## Run cmdline
10 python -m straindesign analyzing-model
11 @CMD_INPUT_MODEL@
12 @CMD_INPUT_MEDIUM@
13 @CMD_BIOMASS_RXN_ID@
14 @CMD_TARGET_RXN_ID@
15 @CMD_INPUT_PATHWAY@
16 #if str('$substrate_cond.substrate_param') == 'yes'
17 --substrate-rxn-id '$substrate_cond.substrate_rxn_id'
18 #end if
19 --output-pareto-png '$output_png'
20 ]]></command>
21 <expand macro="env_variables"/>
22 <inputs>
23 <expand macro="input_model_sbml"/>
24 <expand macro="input_medium_tsv"/>
25 <expand macro="input_biomass_rxn_id"/>
26 <expand macro="input_target_rxn_id"/>
27 <expand macro="input_pathway_sbml"/>
28 <conditional name="substrate_cond">
29 <param name="substrate_param" type="select" label="Provide a substrate reaction" help="Choose yourself a carbon source or it will be detected automatically">
30 <option value="yes">yes</option>
31 <option value="no" selected="true">No</option>
32 </param>
33 <when value="yes">
34 <expand macro="input_substrate_rxn_id"/>
35 </when>
36 <when value="no"/>
37 </conditional>
38 </inputs>
39 <outputs>
40 <data name="output_png" format="png" label="${tool.name}" />
41 </outputs>
42 <tests>
43 <test>
44 <!-- test 1 -->
45 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
46 <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
47 <param name="target_rxn_id" value="EX_tyrp_e" />
48 <output name="output_png" ftype="png">
49 <assert_contents>
50 <has_size value="34000" delta="4000"/>
51 </assert_contents>
52 </output>
53 </test>
54 <test>
55 <!-- test 2 -->
56 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
57 <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
58 <param name="target_rxn_id" value="EX_tyrp_e" />
59 <param name="substrate_rxn_id" value="EX_glc__D_e" />
60 <output name="output_png" ftype="png">
61 <assert_contents>
62 <has_size value="34000" delta="4000"/>
63 </assert_contents>
64 </output>
65 </test>
66 <test>
67 <!-- test 3 -->
68 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
69 <param name="pathway" ftype="sbml" value="butanol.xml" />
70 <param name="medium" ftype="tabular" value="butanol.tsv" />
71 <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
72 <param name="substrate_rxn_id" value="EX_glc__D_e" />
73 <param name="target_rxn_id" value="EX_1btol_e" />
74 <output name="output_png" ftype="png">
75 <assert_contents>
76 <has_size value="34000" delta="4000"/>
77 </assert_contents>
78 </output>
79 </test>
80 </tests>
81 <help><![CDATA[
82 @HELP_TITLE@
83
84 This tool produces a phenotypic-phase-plane plot given these datas:
85 * model
86 * reaction producing a target
87 * biomass reaction
88 These informations are optionals and will be adapted to your needs:
89 * an heterologous pathway
90 * a carbon substrate
91 * media composition
92
93 @HELP_LINK@
94 ]]></help>
95 <expand macro="creator"/>
96 <expand macro="citation"/>
97 </tool>