Mercurial > repos > tduigou > straindesign_simulate_deletion

comparison macros.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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-1:000000000000 0:14747c55330c
1 <macros>
2 <!-- GLOBAL -->
3 <token name="@TOOL_VERSION@">3.2.2</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@LICENSE@">MIT</token>
6 <xml name="requirements">
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">straindesign</requirement>
9 <yield/>
10 </requirements>
11 </xml>
12 <xml name="stdio">
13 <stdio>
14 <regex match="WARNING" level="warning" />
15 <regex match="ERROR" level="fatal" />
16 </stdio>
17 </xml>
18 <xml name="citation">
19 <citations>
20 <citation type="doi">10.1038/s41467-022-32661-x</citation>
21 </citations>
22 </xml>
23 <xml name="creator">
24 <creator>
25 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
26 </creator>
27 </xml>
28 <xml name="env_variables">
29 <environment_variables>
30 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
31 <environment_variable name="USERNAME">\$__user_email__</environment_variable>
32 </environment_variables>
33 </xml>
34
35 <!-- CMDLINE -->
36 <token name="@CMD_INPUT_MODEL@"><![CDATA[
37 --input-model-file '$model'
38 ]]></token>
39 <token name="@CMD_INPUT_PATHWAY@"><![CDATA[
40 #if $pathway
41 --input-pathway-file '$pathway'
42 #end if
43 ]]></token>
44 <token name="@CMD_INPUT_MEDIUM@"><![CDATA[
45 #if $medium
46 --input-medium-file '$medium'
47 #end if
48 ]]></token>
49 <token name="@CMD_BIOMASS_RXN_ID@"><![CDATA[
50 --biomass-rxn-id '$biomass_rxn_id'
51 ]]></token>
52 <token name="@CMD_TARGET_RXN_ID@"><![CDATA[
53 --target-rxn-id '$target_rxn_id'
54 ]]></token>
55
56 <!-- INPUT -->
57 <xml name="input_model_sbml">
58 <param name="model" type="data" format="sbml" label="Model" help="SBML input file, model"/>
59 </xml>
60 <xml name="input_pathway_sbml">
61 <param name="pathway" type="data" format="sbml" optional="True" label="Pathway" help="SBML input file, containing heterologous pathway"/>
62 </xml>
63 <xml name="input_medium_tsv">
64 <param name="medium" type="data" format="tabular" optional="True" label="Medium file" help="TSV input file, no header, with three columns: reaction_id, lower_bound, upper_bound"/>
65 </xml>
66 <xml name="input_biomass_rxn_id">
67 <param name="biomass_rxn_id" type="text" value="" label="Biomass reaction ID" help="Reaction ID contains no special characters">
68 <validator type="empty_field" message="Biomass reaction ID is required"/>
69 <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
70 </param>
71 </xml>
72 <xml name="input_target_rxn_id">
73 <param name="target_rxn_id" type="text" value="" label="Target reaction ID" help="Reaction ID contains no special characters">
74 <validator type="empty_field" message="Target reaction ID is required"/>
75 <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
76 </param>
77 </xml>
78 <xml name="input_substrate_rxn_id">
79 <param name="substrate_rxn_id" type="text" value="" label="Substrate reaction ID" help="Reaction ID contains no special characters">
80 <validator type="empty_field" message="Target reaction ID is required"/>
81 <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
82 </param>
83 </xml>
84
85 <!-- HELP -->
86 <token name="@HELP_TITLE@"><![CDATA[
87 StrainDesign
88 ============
89 ]]></token>
90 <token name="@HELP_LINK@"><![CDATA[
91 Project Links
92 -------------
93
94 * `straindesign <https://github.com/brsynth/straindesign>`_
95 * `cameo <https://github.com/biosustain/cameo>`_
96 ]]></token>
97 </macros>