# HG changeset patch
# User iuc
# Date 1664738853 0
# Node ID 78b7443af284fc0f6dcbf9064c0717a8198dbc44
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
diff -r 000000000000 -r 78b7443af284 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sun Oct 02 19:27:33 2022 +0000
@@ -0,0 +1,97 @@
+
+
+ 3.1.0
+ 1
+ MIT
+
+
+ straindesign
+
+
+
+
+
+
+
+
+
+
+
+ 10.1038/s41467-022-32661-x
+
+
+
+
+
+
+
+
+
+ \$_GALAXY_JOB_TMP_DIR
+ \$__user_email__
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ^(?:[a-zA-Z_])(?:[\w.-])*$
+
+
+
+
+
+ ^(?:[a-zA-Z_])(?:[\w.-])*$
+
+
+
+
+
+ ^(?:[a-zA-Z_])(?:[\w.-])*$
+
+
+
+
+
+`_
+* `cameo `_
+]]>
+
diff -r 000000000000 -r 78b7443af284 reduce-model.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/reduce-model.xml Sun Oct 02 19:27:33 2022 +0000
@@ -0,0 +1,100 @@
+
+ Delete gene in a biological model
+
+ macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ^(?:[ \w.-])*$
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 78b7443af284 test-data/butanol.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/butanol.tsv Sun Oct 02 19:27:33 2022 +0000
@@ -0,0 +1,2 @@
+EX_glc__D_e -10.0 10.0
+EX_o2_e -5.0 5.0
diff -r 000000000000 -r 78b7443af284 test-data/butanol.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/butanol.xml Sun Oct 02 19:27:33 2022 +0000
@@ -0,0 +1,496 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 78b7443af284 test-data/iAF1260.xml.gz
Binary file test-data/iAF1260.xml.gz has changed
diff -r 000000000000 -r 78b7443af284 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 Sun Oct 02 19:27:33 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