# HG changeset patch
# User bgruening
# Date 1721747347 0
# Node ID 7ccc6234b54e5460a7513621378685bb82bcf76a
# Parent 1ac12c0cc7a051ce66fccea50a896903f75bc5e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cpat commit a447bd0404d45c185c4410dc9620e970d6995925
diff -r 1ac12c0cc7a0 -r 7ccc6234b54e cpat.xml
--- a/cpat.xml Mon Jan 29 10:44:49 2024 +0000
+++ b/cpat.xml Tue Jul 23 15:09:07 2024 +0000
@@ -2,21 +2,24 @@
coding potential assessment
3.0.5
- 0
+ 1
cpat
cpat --version
'./hexamer.tsv' &&
@@ -24,7 +27,7 @@
-x './hexamer.tsv'
-c './conding_sequences.${cod_ext}'
-n './nonconding_sequences.${ncod_ext}'
- -r './referece.${ref_ext}'
+ -r './referece.fasta'
--start='${start}'
--stop='${stop}'
--min-orf=$min_orf_model
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@@ -82,7 +98,10 @@
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@@ -114,7 +133,10 @@
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@@ -144,6 +166,41 @@
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+#
+#So, all_fasta.loc could look something like this:
+test1 "Test Genome" ${__HERE__}/test1.fasta.gz
\ No newline at end of file
diff -r 1ac12c0cc7a0 -r 7ccc6234b54e test-data/test03_no_orgs.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test03_no_orgs.txt Tue Jul 23 15:09:07 2024 +0000
@@ -0,0 +1,1 @@
+ENST00000637839.1
diff -r 1ac12c0cc7a0 -r 7ccc6234b54e tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Tue Jul 23 15:09:07 2024 +0000
@@ -0,0 +1,10 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+#test1 Test-Genome ./test-data/test1.fa.gz
\ No newline at end of file
diff -r 1ac12c0cc7a0 -r 7ccc6234b54e tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Jul 23 15:09:07 2024 +0000
@@ -0,0 +1,7 @@
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\ No newline at end of file
diff -r 1ac12c0cc7a0 -r 7ccc6234b54e tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Tue Jul 23 15:09:07 2024 +0000
@@ -0,0 +1,8 @@
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\ No newline at end of file