# HG changeset patch # User devteam # Date 1568209319 14400 # Node ID 2051602a5f97c50ae2f20cd65d454083ad868123 # Parent de2db1bdfbf8fc07b304a7d4c569b6f70bc0064a "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65" diff -r de2db1bdfbf8 -r 2051602a5f97 fasta_compute_length.xml --- a/fasta_compute_length.xml Wed Nov 11 12:13:18 2015 -0500 +++ b/fasta_compute_length.xml Wed Sep 11 09:41:59 2019 -0400 @@ -1,12 +1,50 @@ - + + - fasta_compute_length.py $input $output $keep_first $keep_first_word + + #if $ref.ref_source == 'dbkey': + cp '${ref.index.fields.len_path}' '$output' + #else: + python $__tool_directory__/fasta_compute_length.py + #if $ref.ref_source == 'history': + '$input' + #else: + '${ref.index.fields.path}' + #end if + '$output' + $ref.keep_first + $ref.keep_first_word + #end if + - - - + + + + + + + + + + + + + + + + + + + + + + + + @@ -14,25 +52,38 @@ - - - + + + - - - + + + - - - + + + + + + + + + + + + + + + + diff -r de2db1bdfbf8 -r 2051602a5f97 test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Wed Sep 11 09:41:59 2019 -0400 @@ -0,0 +1,19 @@ +#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: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# +test_id test_dbkey test display name ${__HERE__}/merged.fa diff -r de2db1bdfbf8 -r 2051602a5f97 test-data/dbkeys.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dbkeys.loc Wed Sep 11 09:41:59 2019 -0400 @@ -0,0 +1,2 @@ +# +test_id Test ${__HERE__}/merged.tab diff -r de2db1bdfbf8 -r 2051602a5f97 test-data/merged.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged.fa Wed Sep 11 09:41:59 2019 -0400 @@ -0,0 +1,7 @@ +>asdf length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_ +CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA +>bsdf length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_ +CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGG +GGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGC +CACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCC +ATTGGTC diff -r de2db1bdfbf8 -r 2051602a5f97 test-data/merged.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged.tab Wed Sep 11 09:41:59 2019 -0400 @@ -0,0 +1,2 @@ +asdf 54 +bsdf 187 diff -r de2db1bdfbf8 -r 2051602a5f97 tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Wed Sep 11 09:41:59 2019 -0400 @@ -0,0 +1,18 @@ +#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: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# diff -r de2db1bdfbf8 -r 2051602a5f97 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Sep 11 09:41:59 2019 -0400 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+
diff -r de2db1bdfbf8 -r 2051602a5f97 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Sep 11 09:41:59 2019 -0400 @@ -0,0 +1,14 @@ + + + + + value, dbkey, name, path + +
+ + + + value, name, len_path + +
+