Mercurial > repos > tduigou > straindesign_reduce_model

annotate reduce-model.xml @ 3:c7cd7aa0ea54 draft default tip

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planemo upload for repository https://github.com/brsynth/straindesign commit 628dbf7f95517f13542059ac4a9de58da440f1c6
author tduigou
date Tue, 23 Jul 2024 19:38:04 +0000
parents 736e61efc537
children
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1 <tool id="straindesign_reduce_model" name="StrainDesign reduce-model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
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2 <description>Delete gene 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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c7cd7aa0ea54 planemo upload for repository https://github.com/brsynth/straindesign commit 628dbf7f95517f13542059ac4a9de58da440f1c6
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7 <!--
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8 <expand macro="stdio"/>
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9 -->
0
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10 <command detect_errors="exit_code"><![CDATA[
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11 python -m straindesign reduce-model
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12 @CMD_INPUT_MODEL@
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13 #if str($sd_strategy.sd_cond) == 'yes'
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14 --input-straindesign-file '$sd_strategy.sd_tsv'
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15 --parameter-strategy-str '$sd_strategy.sd_strategy_str'
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16 #end if
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17 --output-file-sbml '$output_sbml'
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18 #if str($input_gene_str) != ''
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19 --input-gene-str #echo $input_gene_str
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20 #end if
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21 ]]></command>
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22 <expand macro="env_variables"/>
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23 <inputs>
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24 <expand macro="input_model_sbml"/>
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25 <conditional name="sd_strategy">
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26 <param name="sd_cond" type="select" label="Fill with the output of StrainDesign simulate-deletion">
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27 <option value="no" selected="True">no</option>
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28 <option value="yes" >yes</option>
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29 </param>
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30 <when value="yes">
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31 <param name="sd_tsv" type="data" format="tabular" label="StrainDesign simulate-deletion output" help="TSV input file"/>
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32 <param name="sd_strategy_str" type="select" label="Strategy" help="Choose which genes will be deleted automatically">
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33 <option value="yield-max" selected="True">Yield Max</option>
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34 <option value="gene-max">Gene Max</option>
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35 <option value="gene-min"> Gene Min</option>
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36 </param>
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37 </when>
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38 <when value="no"/>
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39 </conditional>
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40 <param name="input_gene_str" type="text" value="" label="Gene IDs" help="Multiple genes are separated by space">
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41 <validator type="regex" message="No special characters allowed">^(?:[ \w.-])*$</validator>
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42 </param>
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43 </inputs>
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44 <outputs>
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45 <data name="output_sbml" format="sbml" label="${tool.name}" />
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46 </outputs>
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47 <tests>
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48 <test>
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49 <!-- test 1 -->
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50 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
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51 <param name="input_gene_str" value="b4208 b4208 b3919"/>
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52 <output name="output_sbml" ftype="sbml">
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53 <assert_contents>
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54 <is_valid_xml/>
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55 <not_has_text text="b4208"/>
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56 <not_has_text text="b3919"/>
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57 </assert_contents>
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58 </output>
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59 </test>
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60 <test>
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61 <!-- test 2 -->
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62 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
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63 <param name="sd_cond" value="yes"/>
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64 <param name="sd_tsv" ftype="tabular" value="simulate_deletion.butanol.iAF1260.tsv"/>
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65 <output name="output_sbml" ftype="sbml">
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66 <assert_contents>
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67 <is_valid_xml/>
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68 <not_has_text text="b3919"/>
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69 <not_has_text text="b0529"/>
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70 </assert_contents>
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71 </output>
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72 </test>
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73 <test>
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74 <!-- test 3 -->
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75 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
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76 <param name="sd_cond" value="yes"/>
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77 <param name="sd_tsv" ftype="tabular" value="simulate_deletion.butanol.iAF1260.tsv"/>
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78 <param name="input_gene_str" value="b4208 b4208 b3919"/>
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79 <output name="output_sbml" ftype="sbml">
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80 <assert_contents>
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81 <is_valid_xml/>
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82 <not_has_text text="b4208"/>
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83 <not_has_text text="b3919"/>
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84 <not_has_text text="b0529"/>
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85 </assert_contents>
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86 </output>
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87 </test>
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88 </tests>
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89 <help><![CDATA[
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90 @HELP_TITLE@
736e61efc537 "planemo upload for repository https://github.com/brsynth/straindesign commit 414fd919a5faf8b791859d1f6bf6b2395b952b9a-dirty"
tduigou
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91
736e61efc537 "planemo upload for repository https://github.com/brsynth/straindesign commit 414fd919a5faf8b791859d1f6bf6b2395b952b9a-dirty"
tduigou
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92 This tool deletes some genes provided either from **simulate-deletion¨** or provided by their ids, in a biological model (SBML format).
736e61efc537 "planemo upload for repository https://github.com/brsynth/straindesign commit 414fd919a5faf8b791859d1f6bf6b2395b952b9a-dirty"
tduigou
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93 If you provide a TSV file coming from the **simulate-deletion** commands either the file is cleanned by hand and contains one line or the program tries to identify which genes will be deleted by applying the suited strategy:
736e61efc537 "planemo upload for repository https://github.com/brsynth/straindesign commit 414fd919a5faf8b791859d1f6bf6b2395b952b9a-dirty"
tduigou
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94 * yield-max: the combination of genes with the maximum amount of yiel is taken
736e61efc537 "planemo upload for repository https://github.com/brsynth/straindesign commit 414fd919a5faf8b791859d1f6bf6b2395b952b9a-dirty"
tduigou
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95 * gene-max: the combination of genes with the maximum number of genes is taken
736e61efc537 "planemo upload for repository https://github.com/brsynth/straindesign commit 414fd919a5faf8b791859d1f6bf6b2395b952b9a-dirty"
tduigou
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96 * gene-min: the combination of genes with the minimum number of genes is taken
736e61efc537 "planemo upload for repository https://github.com/brsynth/straindesign commit 414fd919a5faf8b791859d1f6bf6b2395b952b9a-dirty"
tduigou
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97
736e61efc537 "planemo upload for repository https://github.com/brsynth/straindesign commit 414fd919a5faf8b791859d1f6bf6b2395b952b9a-dirty"
tduigou
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98 @HELP_LINK@
736e61efc537 "planemo upload for repository https://github.com/brsynth/straindesign commit 414fd919a5faf8b791859d1f6bf6b2395b952b9a-dirty"
tduigou
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99 ]]></help>
736e61efc537 "planemo upload for repository https://github.com/brsynth/straindesign commit 414fd919a5faf8b791859d1f6bf6b2395b952b9a-dirty"
tduigou
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100 <expand macro="creator"/>
736e61efc537 "planemo upload for repository https://github.com/brsynth/straindesign commit 414fd919a5faf8b791859d1f6bf6b2395b952b9a-dirty"
tduigou
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101 <expand macro="citation"/>
736e61efc537 "planemo upload for repository https://github.com/brsynth/straindesign commit 414fd919a5faf8b791859d1f6bf6b2395b952b9a-dirty"
tduigou
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102 </tool>