# HG changeset patch
# User ggricourt
# Date 1664477297 0
# Node ID 233d87b56795f62c098ae0775edc1140b4eaba09
"planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"
diff -r 000000000000 -r 233d87b56795 analyzing-model.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/analyzing-model.xml Thu Sep 29 18:48:17 2022 +0000
@@ -0,0 +1,98 @@
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+ Produce a pareto plot for a model.
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+ macros.xml
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diff -r 000000000000 -r 233d87b56795 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Sep 29 18:48:17 2022 +0000
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+ 3.1.0
+ 1
+ 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 `_
+]]>
+
diff -r 000000000000 -r 233d87b56795 reduce-model.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/reduce-model.xml Thu Sep 29 18:48:17 2022 +0000
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+ Delete genes and associated reactions in a model.
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+ macros.xml
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+ ^(?:[ \w.-])*$
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diff -r 000000000000 -r 233d87b56795 simulate-deletion.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/simulate-deletion.xml Thu Sep 29 18:48:17 2022 +0000
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+ Optimize the production of a compound by deleting genes in a model.
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+ macros.xml
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+ ^(?:[a-zA-Z_])(?:[\w.-])*$
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diff -r 000000000000 -r 233d87b56795 test-data/butanol.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/butanol.tsv Thu Sep 29 18:48:17 2022 +0000
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+EX_glc__D_e -10.0 10.0
+EX_o2_e -5.0 5.0
diff -r 000000000000 -r 233d87b56795 test-data/butanol.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/butanol.xml Thu Sep 29 18:48:17 2022 +0000
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diff -r 000000000000 -r 233d87b56795 test-data/iAF1260.xml.gz
Binary file test-data/iAF1260.xml.gz has changed
diff -r 000000000000 -r 233d87b56795 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 Thu Sep 29 18:48:17 2022 +0000
@@ -0,0 +1,6 @@
+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