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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
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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1 <macros>
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2 <!-- GLOBAL -->
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3 <token name="@TOOL_VERSION@">3.1.0</token>
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4 <token name="@VERSION_SUFFIX@">1</token>
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5 <token name="@LICENSE@">MIT</token>
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6 <xml name="requirements">
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">straindesign</requirement>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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9 <yield/>
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10 </requirements>
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11 </xml>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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12 <xml name="stdio">
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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13 <stdio>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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14 <regex match="WARNING" level="warning" />
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15 <regex match="ERROR" level="fatal" />
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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16 </stdio>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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17 </xml>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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18 <xml name="citation">
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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19 <citations>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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20 <citation type="doi">10.1038/s41467-022-32661-x</citation>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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21 </citations>
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22 </xml>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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23 <xml name="creator">
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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24 <creator>
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25 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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26 </creator>
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27 </xml>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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28 <xml name="env_variables">
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29 <environment_variables>
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30 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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31 <environment_variable name="USERNAME">\$__user_email__</environment_variable>
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32 </environment_variables>
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33 </xml>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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34
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35 <!-- CMDLINE -->
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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36 <token name="@CMD_INPUT_MODEL@"><![CDATA[
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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37 --input-model-file '$model'
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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38 ]]></token>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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39 <token name="@CMD_INPUT_PATHWAY@"><![CDATA[
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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40 #if $pathway:
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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41 --input-pathway-file '$pathway'
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42 #end if
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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43 ]]></token>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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44 <token name="@CMD_INPUT_MEDIUM@"><![CDATA[
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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45 #if $medium:
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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46 --input-medium-file '$medium'
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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47 #end if
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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48 ]]></token>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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49 <token name="@CMD_BIOMASS_RXN_ID@"><![CDATA[
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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50 --biomass-rxn-id '$biomass_rxn_id'
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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51 ]]></token>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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52 <token name="@CMD_TARGET_RXN_ID@"><![CDATA[
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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53 --target-rxn-id '$target_rxn_id'
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54 ]]></token>
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55
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56 <!-- INPUT -->
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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57 <xml name="input_model_sbml">
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58 <param name="model" type="data" format="sbml" label="Chassis model file"/>
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59 </xml>
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60 <xml name="input_pathway_sbml">
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61 <param name="pathway" type="data" format="sbml" optional="True" label="Pathway file"/>
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62 </xml>
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63 <xml name="input_medium_tsv">
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64 <param name="medium" type="data" format="tsv" optional="True" label="Medium file"/>
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65 </xml>
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66 <xml name="input_biomass_rxn_id">
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67 <param name="biomass_rxn_id" type="text" value="" label="Biomass reaction ID">
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68 <validator type="empty_field" message="Biomass reaction ID is required"/>
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69 <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
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70 </param>
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71 </xml>
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72 <xml name="input_target_rxn_id">
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73 <param name="target_rxn_id" type="text" value="" label="Target reaction ID">
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74 <validator type="empty_field" message="Target reaction ID is required"/>
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75 <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
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76 </param>
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77 </xml>
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78 <xml name="input_substrate_rxn_id">
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79 <param name="substrate_rxn_id" type="text" value="" label="Substrate reaction ID">
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80 <validator type="empty_field" message="Target reaction ID is required"/>
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81 <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
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82 </param>
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83 </xml>
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84
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
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85 <!-- OUTPUT -->
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86 <xml name="output_simulate_deletion">
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87 <data name="output_tsv" format="tsv" label="${tool.name}(${input_strategy.strategy})" />
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88 </xml>
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89
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90 <!-- HELP -->
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91 <token name="@HELP_TITLE@"><![CDATA[
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92 StrainDesign
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93 ============
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94 ]]></token>
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95 <token name="@HELP_LINK@"><![CDATA[
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96 Project Links
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97 -------------
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98
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99 * `straindesign <https://github.com/brsynth/straindesign>`_
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100 * `cameo <https://github.com/biosustain/cameo>`_
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101 ]]></token>
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102 </macros>