Mercurial > repos > tduigou > straindesign_simulate_deletion

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