Mercurial > repos > iuc > straindesign_simulate_deletion
comparison macros.xml @ 0:33c6ffbd098f draft
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
author | iuc |
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date | Sun, 02 Oct 2022 19:26:40 +0000 |
parents | |
children | 1128f1e17c37 |
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-1:000000000000 | 0:33c6ffbd098f |
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1 <macros> | |
2 <!-- GLOBAL --> | |
3 <token name="@TOOL_VERSION@">3.1.0</token> | |
4 <token name="@VERSION_SUFFIX@">1</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> |