Mercurial > repos > tduigou > straindesign_simulate_deletion

annotate macros.xml @ 0:14747c55330c draft

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 38e681e9ebc7bb75ea44f314b48761bf25403420
author tduigou
date Mon, 15 May 2023 14:05:52 +0000
parents
children 6b3e0996185f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
1 <macros>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
2 <!-- GLOBAL -->
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
3 <token name="@TOOL_VERSION@">3.2.2</token>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
4 <token name="@VERSION_SUFFIX@">0</token>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
5 <token name="@LICENSE@">MIT</token>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
6 <xml name="requirements">
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
7 <requirements>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">straindesign</requirement>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
9 <yield/>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
10 </requirements>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
11 </xml>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
12 <xml name="stdio">
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
13 <stdio>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
14 <regex match="WARNING" level="warning" />
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
15 <regex match="ERROR" level="fatal" />
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
16 </stdio>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
17 </xml>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
18 <xml name="citation">
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
19 <citations>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
20 <citation type="doi">10.1038/s41467-022-32661-x</citation>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
21 </citations>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
22 </xml>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
23 <xml name="creator">
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
24 <creator>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
25 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
26 </creator>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
27 </xml>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
28 <xml name="env_variables">
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
29 <environment_variables>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
30 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
31 <environment_variable name="USERNAME">\$__user_email__</environment_variable>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
32 </environment_variables>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
33 </xml>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
34
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
35 <!-- CMDLINE -->
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
36 <token name="@CMD_INPUT_MODEL@"><![CDATA[
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
37 --input-model-file '$model'
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
38 ]]></token>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
39 <token name="@CMD_INPUT_PATHWAY@"><![CDATA[
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
40 #if $pathway
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
41 --input-pathway-file '$pathway'
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
42 #end if
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
43 ]]></token>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
44 <token name="@CMD_INPUT_MEDIUM@"><![CDATA[
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
45 #if $medium
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
46 --input-medium-file '$medium'
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
47 #end if
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
48 ]]></token>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
49 <token name="@CMD_BIOMASS_RXN_ID@"><![CDATA[
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
50 --biomass-rxn-id '$biomass_rxn_id'
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
51 ]]></token>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
52 <token name="@CMD_TARGET_RXN_ID@"><![CDATA[
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
53 --target-rxn-id '$target_rxn_id'
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
54 ]]></token>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
55
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
56 <!-- INPUT -->
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
57 <xml name="input_model_sbml">
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
58 <param name="model" type="data" format="sbml" label="Model" help="SBML input file, model"/>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
59 </xml>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
60 <xml name="input_pathway_sbml">
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
61 <param name="pathway" type="data" format="sbml" optional="True" label="Pathway" help="SBML input file, containing heterologous pathway"/>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
62 </xml>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
63 <xml name="input_medium_tsv">
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
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"/>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
65 </xml>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
66 <xml name="input_biomass_rxn_id">
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
67 <param name="biomass_rxn_id" type="text" value="" label="Biomass reaction ID" help="Reaction ID contains no special characters">
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
68 <validator type="empty_field" message="Biomass reaction ID is required"/>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
69 <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
70 </param>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
71 </xml>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
72 <xml name="input_target_rxn_id">
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
73 <param name="target_rxn_id" type="text" value="" label="Target reaction ID" help="Reaction ID contains no special characters">
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
74 <validator type="empty_field" message="Target reaction ID is required"/>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
75 <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
76 </param>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
77 </xml>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
78 <xml name="input_substrate_rxn_id">
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
79 <param name="substrate_rxn_id" type="text" value="" label="Substrate reaction ID" help="Reaction ID contains no special characters">
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
80 <validator type="empty_field" message="Target reaction ID is required"/>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
81 <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
82 </param>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
83 </xml>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
84
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
85 <!-- HELP -->
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
86 <token name="@HELP_TITLE@"><![CDATA[
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
87 StrainDesign
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
88 ============
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
89 ]]></token>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
90 <token name="@HELP_LINK@"><![CDATA[
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
91 Project Links
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
92 -------------
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
93
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
94 * `straindesign <https://github.com/brsynth/straindesign>`_
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
95 * `cameo <https://github.com/biosustain/cameo>`_
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
96 ]]></token>
14747c55330c planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
tduigou
parents:
diff changeset
97 </macros>