# HG changeset patch
# User tduigou
# Date 1684159552 0
# Node ID 14747c55330cbcc6c7bfc4d000c825f1495f5a69
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
diff -r 000000000000 -r 14747c55330c config/tool_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/config/tool_conf.xml Mon May 15 14:05:52 2023 +0000
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diff -r 000000000000 -r 14747c55330c macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon May 15 14:05:52 2023 +0000
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+ 3.2.2
+ 0
+ MIT
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+ straindesign
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+ 10.1038/s41467-022-32661-x
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+ \$_GALAXY_JOB_TMP_DIR
+ \$__user_email__
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+ ^(?:[a-zA-Z_])(?:[\w.-])*$
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+ ^(?:[a-zA-Z_])(?:[\w.-])*$
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+ ^(?:[a-zA-Z_])(?:[\w.-])*$
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+`_
+* `cameo `_
+]]>
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diff -r 000000000000 -r 14747c55330c simulate-deletion.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/simulate-deletion.xml Mon May 15 14:05:52 2023 +0000
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+ Search genes to delete in a biological model
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+ macros.xml
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+ ^(?:[a-zA-Z_])(?:[\w.-])*$
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diff -r 000000000000 -r 14747c55330c test-data/butanol.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/butanol.tsv Mon May 15 14:05:52 2023 +0000
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+EX_glc__D_e -10.0 10.0
+EX_o2_e -5.0 5.0
diff -r 000000000000 -r 14747c55330c test-data/butanol.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/butanol.xml Mon May 15 14:05:52 2023 +0000
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diff -r 000000000000 -r 14747c55330c test-data/iAF1260.xml.gz
Binary file test-data/iAF1260.xml.gz has changed
diff -r 000000000000 -r 14747c55330c test-data/simulate_deletion.butanol.iAF1260.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/simulate_deletion.butanol.iAF1260.tsv Mon May 15 14:05:52 2023 +0000
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+reactions genes size fva_min fva_max target_flux biomass_flux yield fitness
+"('ATPS4rpp',)" "(('b3735',), ('b3734',), ('b3736',), ('b3731',), ('b3732',))" 1 0.0 0.00641204819277442 0.0 0.2199110076152308 0.0 0.0
+"('TPI',)" "(('b3919',),)" 1 0.0 0.006455168431418056 0.0 0.0 0.0 0.0
+"('ALAt2pp', 'DSERt2pp', 'DALAt2pp', 'BALAt2pp', 'TPI')" "(('b4208', 'b3919'),)" 2 0.0 0.006455167733784362 0.0 0.0 0.0 0.0
+"('OPHHX', 'TPI')" "(('b3835', 'b3919'),)" 2 0.0 0.006455168423924535 0.0 0.0 0.0 0.0
+"('TPI', 'MTHFC', 'MTHFD')" "(('b0529', 'b3919'),('b3919', 'b0529'))" 2 0.0 0.006455095014414326 0.0 0.0 1.2 0.0