# HG changeset patch # User blankenberg # Date 1575564920 0 # Node ID f297269cbcd8bdb97d94dd77bcd277f9dc7d486c # Parent dac6381febb71398098d742337fec3aa119a2277 "planemo upload for repository https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/master/tools/naive_variant_caller commit 6f2b4ed336036cd98c043536e45905bcd3c93044" diff -r dac6381febb7 -r f297269cbcd8 naive_variant_caller.xml --- a/naive_variant_caller.xml Tue Apr 03 10:50:29 2018 -0400 +++ b/naive_variant_caller.xml Thu Dec 05 16:55:20 2019 +0000 @@ -59,10 +59,25 @@ - + + - + + + + + + + + + + + + + + + diff -r dac6381febb7 -r f297269cbcd8 tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Thu Dec 05 16:55:20 2019 +0000 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa diff -r dac6381febb7 -r f297269cbcd8 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Tue Apr 03 10:50:29 2018 -0400 +++ b/tool_data_table_conf.xml.sample Thu Dec 05 16:55:20 2019 +0000 @@ -1,5 +1,10 @@ + + value, dbkey, name, path + +
+ line_type, value, path