Mercurial > repos > iuc > straindesign_reduce_model

comparison reduce-model.xml @ 0:30b18a004226 draft

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planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
author iuc
date Sun, 02 Oct 2022 19:25:32 +0000
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1 <tool id="straindesign_reduce_model" name="StrainDesign reduce-model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
2 <description>Delete gene 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 reduce-model
10 @CMD_INPUT_MODEL@
11 #if str($sd_strategy.sd_cond) == 'yes'
12 --input-straindesign-file '$sd_strategy.sd_tsv'
13 --parameter-strategy-str '$sd_strategy.sd_strategy_str'
14 #end if
15 --output-file-sbml '$output_sbml'
16 #if str($input_gene_str) != ''
17 --input-gene-str #echo $input_gene_str
18 #end if
19 ]]></command>
20 <expand macro="env_variables"/>
21 <inputs>
22 <expand macro="input_model_sbml"/>
23 <conditional name="sd_strategy">
24 <param name="sd_cond" type="select" label="Fill with the output of StrainDesign simulate-deletion">
25 <option value="no" selected="True">no</option>
26 <option value="yes" >yes</option>
27 </param>
28 <when value="yes">
29 <param name="sd_tsv" type="data" format="tabular" label="StrainDesign simulate-deletion output" help="TSV input file"/>
30 <param name="sd_strategy_str" type="select" label="Strategy" help="Choose which genes will be deleted automatically">
31 <option value="yield-max" selected="True">Yield Max</option>
32 <option value="gene-max">Gene Max</option>
33 <option value="gene-min"> Gene Min</option>
34 </param>
35 </when>
36 <when value="no"/>
37 </conditional>
38 <param name="input_gene_str" type="text" value="" label="Gene IDs" help="Multiple genes are separated by space">
39 <validator type="regex" message="No special characters allowed">^(?:[ \w.-])*$</validator>
40 </param>
41 </inputs>
42 <outputs>
43 <data name="output_sbml" format="sbml" label="${tool.name}" />
44 </outputs>
45 <tests>
46 <test>
47 <!-- test 1 -->
48 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
49 <param name="input_gene_str" value="b4208 b4208 b3919"/>
50 <output name="output_sbml" ftype="sbml">
51 <assert_contents>
52 <is_valid_xml/>
53 <not_has_text text="b4208"/>
54 <not_has_text text="b3919"/>
55 </assert_contents>
56 </output>
57 </test>
58 <test>
59 <!-- test 2 -->
60 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
61 <param name="sd_cond" value="yes"/>
62 <param name="sd_tsv" ftype="tabular" value="simulate_deletion.butanol.iAF1260.tsv"/>
63 <output name="output_sbml" ftype="sbml">
64 <assert_contents>
65 <is_valid_xml/>
66 <not_has_text text="b3919"/>
67 <not_has_text text="b0529"/>
68 </assert_contents>
69 </output>
70 </test>
71 <test>
72 <!-- test 3 -->
73 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
74 <param name="sd_cond" value="yes"/>
75 <param name="sd_tsv" ftype="tabular" value="simulate_deletion.butanol.iAF1260.tsv"/>
76 <param name="input_gene_str" value="b4208 b4208 b3919"/>
77 <output name="output_sbml" ftype="sbml">
78 <assert_contents>
79 <is_valid_xml/>
80 <not_has_text text="b4208"/>
81 <not_has_text text="b3919"/>
82 <not_has_text text="b0529"/>
83 </assert_contents>
84 </output>
85 </test>
86 </tests>
87 <help><![CDATA[
88 @HELP_TITLE@
89
90 This tool deletes some genes provided either from **simulate-deletion¨** or provided by their ids, in a biological model (SBML format).
91 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:
92 * yield-max: the combination of genes with the maximum amount of yiel is taken
93 * gene-max: the combination of genes with the maximum number of genes is taken
94 * gene-min: the combination of genes with the minimum number of genes is taken
95
96 @HELP_LINK@
97 ]]></help>
98 <expand macro="creator"/>
99 <expand macro="citation"/>
100 </tool>