Mercurial > repos > iuc > straindesign_simulate_deletion

annotate simulate-deletion.xml @ 0:33c6ffbd098f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
author iuc
date Sun, 02 Oct 2022 19:26:40 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
1 <tool id="straindesign_simulate_deletion" name="StrainDesign simulate-deletion" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
2 <description>Search genes to delete in a biological model</description>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
3 <macros>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
4 <import>macros.xml</import>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
5 </macros>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
7 <expand macro="stdio"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
9 python -m straindesign simulate-deletion
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
10 @CMD_INPUT_MODEL@
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
11 @CMD_INPUT_PATHWAY@
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
12 @CMD_INPUT_MEDIUM@
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
13 @CMD_BIOMASS_RXN_ID@
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
14 @CMD_TARGET_RXN_ID@
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
15 --strategy '$input_strategy.strategy'
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
16 #if str($input_strategy.strategy) == 'ko':
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
17 --substrate-rxn-id '$input_strategy.substrate_rxn_id'
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
18 #if $input_strategy.annotate:
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
19 --email '$__user_email__'
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
20 #end if
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
21 #end if
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
22 #if str($max_time_cond.max_time_param) == 'yes':
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
23 --max-time '$max_time_cond.max_time'
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
24 #end if
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
25 --max-knockouts '$max_knockouts'
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
26 --output-file-tsv '$output_tsv'
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
27 ]]></command>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
28 <expand macro="env_variables"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
29 <inputs>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
30 <expand macro="input_model_sbml"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
31 <expand macro="input_pathway_sbml"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
32 <expand macro="input_medium_tsv"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
33 <expand macro="input_biomass_rxn_id"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
34 <expand macro="input_target_rxn_id"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
35 <conditional name="input_strategy">
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
36 <param name="strategy" type="select" label="Strategy" help="Genes or Reactions to delete">
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
37 <option value="ko" selected="True">Gene knockouts</option>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
38 <option value="ou" >Reaction knockouts</option>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
39 </param>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
40 <when value="ko">
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
41 <param name="substrate_rxn_id" type="text" value="" label="Substrate reaction ID" help="Reaction ID contains no special characters">
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
42 <validator type="empty_field" message="Substrate reaction ID is required"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
43 <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
44 </param>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
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"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
46 </when>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
47 <when value="ou">
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
48 </when>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
49 </conditional>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
50 <param name="max_knockouts" type="integer" min="1" max="10" value="3" label="Number of items deleted to consider"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
51 <conditional name="max_time_cond">
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
52 <param name="max_time_param" type="select" label="Time out" help="Limit scan time">
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
53 <option value="no" selected="True">no</option>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
54 <option value="yes" >yes</option>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
55 </param>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
56 <when value="yes">
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
57 <param name="max_time" type="integer" min="5" max="120" value="10" label="minutes"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
58 </when>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
59 <when value="no"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
60 </conditional>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
61 </inputs>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
62 <outputs>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
63 <data name="output_tsv" format="tabular" label="${tool.name}(${input_strategy.strategy})" />
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
64 </outputs>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
65 <tests>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
66 <test>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
67 <!-- test 1 -->
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
68 <param name="model" ftype="sbml" value="iAF1260.xml.gz" />
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
69 <param name="pathway" ftype="sbml" value="butanol.xml" />
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
70 <param name="medium" ftype="tabular" value="butanol.tsv" />
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
71 <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
72 <param name="target_rxn_id" value="EX_1btol_e" />
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
73 <param name="substrate_rxn_id" value="EX_glc__D_e" />
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
74 <param name="max_time_param" value="yes"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
75 <param name="max_time" value="5"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
76 <output name="output_tsv" ftype="tabular">
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
77 <assert_contents>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
78 <has_line_matching expression="^reactions\tgenes\tsize\tfva_min\tfva_max\ttarget_flux\tbiomass_flux\tyield\tfitness$"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
79 </assert_contents>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
80 </output>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
81 </test>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
82 </tests>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
83 <help><![CDATA[
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
84 @HELP_TITLE@
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
85
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
86 This tool helps to identify gene's deletions in a biological model to optimize the reaction of a targeted compound.
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
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".
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
88 The strategies "ko" and "ou" find genes and reactions respectively to delete.
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
89
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
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.
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
91
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
92 @HELP_LINK@
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
93 ]]></help>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
94 <expand macro="creator"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
95 <expand macro="citation"/>
33c6ffbd098f planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
iuc
parents:
diff changeset
96 </tool>