Mercurial > repos > ggricourt > straindesign

annotate reduce-model.xml @ 0:233d87b56795 draft default tip

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 ef548ee3fe2740006c95cafb67504c72ef509575"
author ggricourt
date Thu, 29 Sep 2022 18:48:17 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
1 <tool id="reduce-model" name="reduce-model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
2 <description>Delete genes and associated reactions in a model.</description>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
3 <macros>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
4 <import>macros.xml</import>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
5 </macros>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
6 <expand macro="requirements"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
7 <expand macro="stdio"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
9 python -m straindesign reduce-model
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
10 @CMD_INPUT_MODEL@
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
11 #if $sd_strategy.sd_cond:
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
12 --input-straindesign-file '$sd_strategy.sd_tsv'
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
13 --parameter-strategy-str '$sd_strategy.sd_strategy_str'
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
14 #end if
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
15 --output-file-sbml '$output_sbml'
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
16 #if str($input_gene_str) != ''
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
17 #set $sgs = str($input_gene_str)
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
18 --input-gene-str #echo $sgs
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
19 #end if
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
20 ]]></command>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
21 <expand macro="env_variables"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
22 <inputs>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
23 <expand macro="input_model_sbml"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
24 <conditional name="sd_strategy">
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
25 <param name="sd_cond" type="boolean" checked="false" label="Fill with the output of StrainDesign simulate-deletion"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
26 <when value="true">
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
27 <param name="sd_tsv" type="data" format="tsv" label="StrainDesign simulate-deletion output"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
28 <param name="sd_strategy_str" type="select" label="Strategy">
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
29 <option value="yield-max" selected="True">Yield Max</option>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
30 <option value="gene-max">Gene Max</option>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
31 <option value="gene-min"> Gene Min</option>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
32 </param>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
33 </when>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
34 <when value="false"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
35 </conditional>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
36 <param name="input_gene_str" type="text" value="" label="Gene IDs. Multiple genes are separated by space">
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
37 <validator type="regex" message="No special characters allowed">^(?:[ \w.-])*$</validator>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
38 </param>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
39 </inputs>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
40 <outputs>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
41 <data name="output_sbml" format="sbml" label="${tool.name}" />
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
42 </outputs>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
43 <tests>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
44 <test>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
45 <!-- test 1 -->
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
46 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
47 <param name="input_gene_str" value="b4208 b4208 b3919"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
48 <output name="output_sbml" ftype="sbml">
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
49 <assert_contents>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
50 <is_valid_xml/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
51 <not_has_text text="b4208"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
52 <not_has_text text="b3919"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
53 </assert_contents>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
54 </output>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
55 </test>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
56 <test>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
57 <!-- test 2 -->
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
58 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
59 <param name="sd_cond" value="true"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
60 <param name="sd_tsv" ftype="tabular" value="simulate_deletion.butanol.iAF1260.tsv"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
61 <output name="output_sbml" ftype="sbml">
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
62 <assert_contents>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
63 <is_valid_xml/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
64 <not_has_text text="b3919"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
65 <not_has_text text="b0529"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
66 </assert_contents>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
67 </output>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
68 </test>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
69 <test>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
70 <!-- test 3 -->
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
71 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
72 <param name="sd_cond" value="true"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
73 <param name="sd_tsv" ftype="tabular" value="simulate_deletion.butanol.iAF1260.tsv"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
74 <param name="input_gene_str" value="b4208 b4208 b3919"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
75 <output name="output_sbml" ftype="sbml">
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
76 <assert_contents>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
77 <is_valid_xml/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
78 <not_has_text text="b4208"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
79 <not_has_text text="b3919"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
80 <not_has_text text="b0529"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
81 </assert_contents>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
82 </output>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
83 </test>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
84 </tests>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
85 <help><![CDATA[
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
86 @HELP_TITLE@
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
87
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
88 This tool helps to delete some genes provided either from **simulate-deletion¨** or provided by their ids, in an SBML model.
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
89 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:
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
90 * yield-max: the combination of genes with the maximum amount of yiel is taken
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
91 * gene-max: the combination of genes with the maximum number of genes is taken
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
92 * gene-min: the combination of genes with the minimum number of genes is taken
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
93
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
94 @HELP_LINK@
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
95 ]]></help>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
96 <expand macro="creator"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
97 <expand macro="citation"/>
233d87b56795 "planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
ggricourt
parents:
diff changeset
98 </tool>