Mercurial > repos > shirish > ss_tool
changeset 42:ae2d1916c2d7 draft
Deleted selected files
| author | shirish |
|---|---|
| date | Tue, 03 Jun 2014 07:24:37 -0400 |
| parents | 6d27985904fa |
| children | 417503ae8cd7 |
| files | fasta_indexes.loc.sample softsearch.xml |
| diffstat | 2 files changed, 0 insertions(+), 85 deletions(-) [+] |
line wrap: on
line diff
--- a/fasta_indexes.loc.sample Tue Jun 03 07:24:05 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): -# -# <unique_build_id> <dbkey> <display_name> <file_base_path> -# -#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
--- a/softsearch.xml Tue Jun 03 07:24:05 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -<?xml version="1.0"?> -<tool id="SoftSearch" name="SoftSearch" version="0.6"> - <requirements> - <requirement type="package" version="0.6">softsearch</requirement> - </requirements> - <description>for structure variation</description> - <command>#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 $out_file1 - #end if - </command> - <inputs> - <param name="bam_file" type="data" format="bam" label="BAM Files" /> - <conditional name="source"> - <param name="index_source" type="select" label="Choose the source for the reference list"> - <option value="cached">Locally cached</option> - <option value="history">History</option> - </param> - <when value="history"> - <param format="fasta" name="history_fasta_file" type="data" label="Fasta file from history."/> - </when> - <when value="cached"> - <param name="ref_fasta" type="select" > - <options from_data_table="fasta_indexes"> - <validator type="no_options" message="No Fasta file is available" /> - </options> - </param> - </when> - </conditional> - <param name="inc" type="hidden" value="n=$RANDOM" /> - <param name="min_length_soft_clip" type="integer" value="10" label="-l Minimum length of soft-clipped segment [5]" /> - <param name="min_map_quality" type="integer" value="20" label="-q Minimum mapping quality [20]" /> - <param name="min_depth_soft_clip_loc" type="integer" value="10" label="-r Minimum depth of soft-clipped reads at position [5]" /> - <param name="min_no_discordant_read" type="integer" value="10" label="-m Minimum number of discordant read pairs [5]" /> - <param name="no_sd_consider_discordant" type="integer" value="4" label="-s Number of sd away from mean to be considered discordant" /> - </inputs> - <outputs> - <data format="vcf" name="out_file1" /> - </outputs> - <help> - </help> -</tool> - - - - - - - - - - - - -