Mercurial > repos > tduigou > straindesign_simulate_deletion

annotate simulate-deletion.xml @ 0:14747c55330c draft

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planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
author tduigou
date Mon, 15 May 2023 14:05:52 +0000
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children 6b3e0996185f
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0
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
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1 <tool id="straindesign_simulate_deletion" name="StrainDesign simulate-deletion" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
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2 <description>Search genes to delete in a biological 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 python -m straindesign simulate-deletion
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10 @CMD_INPUT_MODEL@
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11 @CMD_INPUT_PATHWAY@
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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 --strategy '$input_strategy.strategy'
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16 #if str($input_strategy.strategy) == 'ko':
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17 --substrate-rxn-id '$input_strategy.substrate_rxn_id'
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18 #if $input_strategy.annotate:
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19 --email '$__user_email__'
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20 #end if
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21 #end if
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22 #if str($max_time_cond.max_time_param) == 'yes':
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23 --max-time '$max_time_cond.max_time'
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24 #end if
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25 --max-knockouts '$max_knockouts'
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26 --output-file-tsv '$output_tsv'
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27 ]]></command>
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28 <expand macro="env_variables"/>
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29 <inputs>
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30 <expand macro="input_model_sbml"/>
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31 <expand macro="input_pathway_sbml"/>
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32 <expand macro="input_medium_tsv"/>
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33 <expand macro="input_biomass_rxn_id"/>
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34 <expand macro="input_target_rxn_id"/>
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35 <conditional name="input_strategy">
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36 <param name="strategy" type="select" label="Strategy" help="Genes or Reactions to delete">
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37 <option value="ko" selected="True">Gene knockouts</option>
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38 <option value="ou" >Reaction knockouts</option>
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39 </param>
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40 <when value="ko">
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41 <param name="substrate_rxn_id" type="text" value="" label="Substrate reaction ID" help="Reaction ID contains no special characters">
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42 <validator type="empty_field" message="Substrate reaction ID is required"/>
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43 <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
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44 </param>
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45 <param name="annotate" type="boolean" label="Annotate the genes" checked="false" help="Please agree to use your email for query the NCBI website to annotate the genes"/>
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46 </when>
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47 <when value="ou">
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48 </when>
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49 </conditional>
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50 <param name="max_knockouts" type="integer" min="1" max="10" value="3" label="Number of items deleted to consider"/>
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51 <conditional name="max_time_cond">
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52 <param name="max_time_param" type="select" label="Time out" help="Limit scan time">
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53 <option value="no" selected="True">no</option>
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54 <option value="yes" >yes</option>
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55 </param>
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56 <when value="yes">
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57 <param name="max_time" type="integer" min="5" max="120" value="10" label="minutes"/>
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58 </when>
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59 <when value="no"/>
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60 </conditional>
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61 </inputs>
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62 <outputs>
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63 <data name="output_tsv" format="tabular" label="${tool.name}(${input_strategy.strategy})" />
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64 </outputs>
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65 <tests>
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66 <test>
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67 <!-- test 1 -->
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68 <param name="model" ftype="sbml" value="iAF1260.xml.gz" />
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69 <param name="pathway" ftype="sbml" value="butanol.xml" />
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70 <param name="medium" ftype="tabular" value="butanol.tsv" />
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71 <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
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72 <param name="target_rxn_id" value="EX_1btol_e" />
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73 <param name="substrate_rxn_id" value="EX_glc__D_e" />
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74 <param name="max_time_param" value="yes"/>
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75 <param name="max_time" value="5"/>
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76 <output name="output_tsv" ftype="tabular">
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77 <assert_contents>
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78 <has_line_matching expression="^reactions\tgenes\tsize\tfva_min\tfva_max\ttarget_flux\tbiomass_flux\tyield\tfitness$"/>
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79 </assert_contents>
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80 </output>
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81 </test>
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82 </tests>
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83 <help><![CDATA[
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84 @HELP_TITLE@
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85
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86 This tool helps to identify gene's deletions in a biological model to optimize the reaction of a targeted compound.
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87 The medium composition can be modified with a TSV file formatted as following: no header, with these columns "reaction id, lower_bound, upper_bound".
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88 The strategies "ko" and "ou" find genes and reactions respectively to delete.
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89
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90 Disclaimer: if you want to annotate the genes with their names, your email address will be used by the library Biopython to request the NCBI website.
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91
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92 @HELP_LINK@
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93 ]]></help>
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94 <expand macro="creator"/>
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95 <expand macro="citation"/>
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96 </tool>