# 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 @@ -46,9 +49,22 @@ - - - + + + + + + + + + + + + + + + + @@ -82,7 +98,10 @@ - + + + + @@ -114,7 +133,10 @@ - + + + + @@ -144,6 +166,41 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +# +#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 @@ + + + + value, name, path + +
+
\ 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 @@ + + + + + value, name, path + +
+
\ No newline at end of file