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annotate analyzing-model.xml @ 0:233d87b56795 draft default tip

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"planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
author ggricourt
date Thu, 29 Sep 2022 18:48:17 +0000
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0
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1 <tool id="analyzing-model" name="analyzing-model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
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2 <description>Produce a pareto plot for a model.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ## Run cmdline
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10 python -m straindesign analyzing-model
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11 @CMD_INPUT_MODEL@
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12 @CMD_INPUT_MEDIUM@
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13 @CMD_BIOMASS_RXN_ID@
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14 @CMD_TARGET_RXN_ID@
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15 @CMD_INPUT_PATHWAY@
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16 #if str('$substrate_cond.substrate_param') == 'yes':
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17 --substrate-rxn-id '$substrate_cond.substrate_rxn_id'
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18 #end if
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19 --output-pareto-png '$output_png'
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20 ]]></command>
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21 <expand macro="env_variables"/>
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22 <inputs>
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23 <expand macro="input_model_sbml"/>
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24 <expand macro="input_medium_tsv"/>
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25 <expand macro="input_biomass_rxn_id"/>
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26 <expand macro="input_target_rxn_id"/>
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27 <expand macro="input_pathway_sbml"/>
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28 <conditional name="substrate_cond">
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29 <param name="substrate_param" type="select" label="Provide a substrate reaction">
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30 <option value="yes">yes</option>
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31 <option value="no" selected="true">No</option>
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32 </param>
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33 <when value="yes">
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34 <expand macro="input_substrate_rxn_id"/>
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35 </when>
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36 <when value="no">
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37 </when>
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38 </conditional>
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39 </inputs>
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40 <outputs>
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41 <data name="output_png" format="png" label="${tool.name}" />
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42 </outputs>
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43 <tests>
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44 <test>
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45 <!-- test 1 -->
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46 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
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47 <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
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48 <param name="target_rxn_id" value="EX_tyrp_e" />
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49 <output name="output_png" ftype="png">
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50 <assert_contents>
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51 <has_size value="34000" delta="4000"/>
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52 </assert_contents>
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53 </output>
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54 </test>
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55 <test>
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56 <!-- test 2 -->
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57 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
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58 <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
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59 <param name="target_rxn_id" value="EX_tyrp_e" />
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60 <param name="substrate_rxn_id" value="EX_glc__D_e" />
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61 <output name="output_png" ftype="png">
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62 <assert_contents>
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63 <has_size value="34000" delta="4000"/>
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64 </assert_contents>
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65 </output>
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66 </test>
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67 <test>
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68 <!-- test 3 -->
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69 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
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70 <param name="pathway" ftype="sbml" value="butanol.xml" />
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71 <param name="medium" ftype="tabular" value="butanol.tsv" />
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72 <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
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73 <param name="substrate_rxn_id" value="EX_glc__D_e" />
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74 <param name="target_rxn_id" value="EX_1btol_e" />
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75 <output name="output_png" ftype="png">
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76 <assert_contents>
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77 <has_size value="34000" delta="4000"/>
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78 </assert_contents>
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79 </output>
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80 </test>
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81 </tests>
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82 <help><![CDATA[
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83 @HELP_TITLE@
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84
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85 This tool produces a phenotypic-phase-plane plot given these datas:
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86 * model
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87 * reaction producing a target
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88 * biomass reaction
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89 These informations are optionals and will be adapted to your needs:
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90 * an heterologous pathway
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91 * a carbon substrate
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92 * media composition
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93
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94 @HELP_LINK@
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95 ]]></help>
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96 <expand macro="creator"/>
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97 <expand macro="citation"/>
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98 </tool>