# HG changeset patch # User priti # Date 1401964816 14400 # Node ID a9c96471b9dbfb849baba2e2561fd5402aeebd52 # Parent 49c82df34f1ac5b67bd40f27da6c39b7393dcbae Deleted selected files diff -r 49c82df34f1a -r a9c96471b9db test-data/fasta_indexes.loc.sample --- a/test-data/fasta_indexes.loc.sample Thu Jun 05 03:27:27 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -#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 49c82df34f1a -r a9c96471b9db test-data/tool_data_table_conf.xml.sample --- a/test-data/tool_data_table_conf.xml.sample Thu Jun 05 03:27:27 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ - - - - - 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 49c82df34f1a -r a9c96471b9db tool_dependencies.xml --- a/tool_dependencies.xml Thu Jun 05 03:27:27 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - - diff -r 49c82df34f1a -r a9c96471b9db vdt_wrapper.xml --- a/vdt_wrapper.xml Thu Jun 05 03:27:27 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ - - - - vdt - - for structure variation - #if $source.index_source=="history" - samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | 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.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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -