Mercurial > repos > tduigou > straindesign_reduce_model
annotate reduce-model.xml @ 2:3119eda6ff48 draft default tip
planemo upload for repository https://github.com/brsynth/straindesign commit 628dbf7f95517f13542059ac4a9de58da440f1c6
author | tduigou |
---|---|
date | Tue, 23 Jul 2024 19:26:11 +0000 |
parents | 2af5552f2273 |
children |
rev | line source |
---|---|
0
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
1 <tool id="straindesign_reduce_model" name="StrainDesign reduce-model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@"> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
2 <description>Delete gene in a biological model</description> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
3 <macros> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
4 <import>macros.xml</import> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
5 </macros> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
6 <expand macro="requirements"/> |
2
3119eda6ff48
planemo upload for repository https://github.com/brsynth/straindesign commit 628dbf7f95517f13542059ac4a9de58da440f1c6
tduigou
parents:
0
diff
changeset
|
7 <!-- |
0
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
8 <expand macro="stdio"/> |
2
3119eda6ff48
planemo upload for repository https://github.com/brsynth/straindesign commit 628dbf7f95517f13542059ac4a9de58da440f1c6
tduigou
parents:
0
diff
changeset
|
9 --> |
0
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
10 <command detect_errors="exit_code"><![CDATA[ |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
11 python -m straindesign reduce-model |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
12 @CMD_INPUT_MODEL@ |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
13 #if str($sd_strategy.sd_cond) == 'yes' |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
14 --input-straindesign-file '$sd_strategy.sd_tsv' |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
15 --parameter-strategy-str '$sd_strategy.sd_strategy_str' |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
16 #end if |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
17 --output-file-sbml '$output_sbml' |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
18 #if str($input_gene_str) != '' |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
19 --input-gene-str #echo $input_gene_str |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
20 #end if |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
21 ]]></command> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
22 <expand macro="env_variables"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
23 <inputs> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
24 <expand macro="input_model_sbml"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
25 <conditional name="sd_strategy"> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
26 <param name="sd_cond" type="select" label="Fill with the output of StrainDesign simulate-deletion"> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
27 <option value="no" selected="True">no</option> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
28 <option value="yes" >yes</option> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
29 </param> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
30 <when value="yes"> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
31 <param name="sd_tsv" type="data" format="tabular" label="StrainDesign simulate-deletion output" help="TSV input file"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
32 <param name="sd_strategy_str" type="select" label="Strategy" help="Choose which genes will be deleted automatically"> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
33 <option value="yield-max" selected="True">Yield Max</option> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
34 <option value="gene-max">Gene Max</option> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
35 <option value="gene-min"> Gene Min</option> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
36 </param> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
37 </when> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
38 <when value="no"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
39 </conditional> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
40 <param name="input_gene_str" type="text" value="" label="Gene IDs" help="Multiple genes are separated by space"> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
41 <validator type="regex" message="No special characters allowed">^(?:[ \w.-])*$</validator> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
42 </param> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
43 </inputs> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
44 <outputs> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
45 <data name="output_sbml" format="sbml" label="${tool.name}" /> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
46 </outputs> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
47 <tests> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
48 <test> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
49 <!-- test 1 --> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
50 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
51 <param name="input_gene_str" value="b4208 b4208 b3919"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
52 <output name="output_sbml" ftype="sbml"> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
53 <assert_contents> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
54 <is_valid_xml/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
55 <not_has_text text="b4208"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
56 <not_has_text text="b3919"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
57 </assert_contents> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
58 </output> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
59 </test> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
60 <test> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
61 <!-- test 2 --> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
62 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
63 <param name="sd_cond" value="yes"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
64 <param name="sd_tsv" ftype="tabular" value="simulate_deletion.butanol.iAF1260.tsv"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
65 <output name="output_sbml" ftype="sbml"> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
66 <assert_contents> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
67 <is_valid_xml/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
68 <not_has_text text="b3919"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
69 <not_has_text text="b0529"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
70 </assert_contents> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
71 </output> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
72 </test> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
73 <test> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
74 <!-- test 3 --> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
75 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
76 <param name="sd_cond" value="yes"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
77 <param name="sd_tsv" ftype="tabular" value="simulate_deletion.butanol.iAF1260.tsv"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
78 <param name="input_gene_str" value="b4208 b4208 b3919"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
79 <output name="output_sbml" ftype="sbml"> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
80 <assert_contents> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
81 <is_valid_xml/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
82 <not_has_text text="b4208"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
83 <not_has_text text="b3919"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
84 <not_has_text text="b0529"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
85 </assert_contents> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
86 </output> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
87 </test> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
88 </tests> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
89 <help><![CDATA[ |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
90 @HELP_TITLE@ |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
91 |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
92 This tool deletes some genes provided either from **simulate-deletion¨** or provided by their ids, in a biological model (SBML format). |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
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: |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
94 * yield-max: the combination of genes with the maximum amount of yiel is taken |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
95 * gene-max: the combination of genes with the maximum number of genes is taken |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
96 * gene-min: the combination of genes with the minimum number of genes is taken |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
97 |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
98 @HELP_LINK@ |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
99 ]]></help> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
100 <expand macro="creator"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
101 <expand macro="citation"/> |
2af5552f2273
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff
changeset
|
102 </tool> |