# HG changeset patch # User priti # Date 1402139728 14400 # Node ID 424cccf87e2b18168a926ce0d229811b1230950b # Parent 32fb5d855364eb05ca7113286e4d12cf6ddb7def Uploaded diff -r 32fb5d855364 -r 424cccf87e2b softsearch_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/softsearch_wrapper.xml Sat Jun 07 07:15:28 2014 -0400 @@ -0,0 +1,56 @@ + + + + softsearch + + for structure variation + #if $source.index_source=="history" + samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | ~//softsearch/0.6/priti/vdt_dependency/40c42b16a426/src/SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.history_fasta_file -o $out_file1 + #else + samtools index $bam_file ; samtools faidx $source.ref_fasta.fields.path ; $inc | ~//softsearch/0.6/priti/vdt_dependency/40c42b16a426/src/SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.ref_fasta.fields.path -o $out_file1 + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 32fb5d855364 -r 424cccf87e2b tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Sat Jun 07 07:15:28 2014 -0400 @@ -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 32fb5d855364 -r 424cccf87e2b tool-data/tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tool_data_table_conf.xml.sample Sat Jun 07 07:15:28 2014 -0400 @@ -0,0 +1,82 @@ + + + + + value, dbkey, name, path + +
+ + + value, dbkey, formats, name, path + +
+ + + value, name, path + +
+ + + value, name, path + +
+ + + value, dbkey, name, path + +
+ + + value, dbkey, name, path + +
+ + + name, value, dbkey, species + +
+ + + value, dbkey, name, path + +
+ + + value, name, path + +
+ + + value, name, path + +
+ + + value, dbkey, name, path + +
+ + + value, dbkey, name, path + +
+ + + value, name, gatk_value, tools_valid_for + +
+ + + value, dbkey, name, path + +
+ + + value, dbkey, name, path + +
+ + value, dbkey, name, path + +
+ diff -r 32fb5d855364 -r 424cccf87e2b tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Jun 07 07:15:28 2014 -0400 @@ -0,0 +1,6 @@ + + + + + +