diff --git a/tool-data/mosaik_index.loc.sample b/tool-data/mosaik_index.loc.sample new file mode 100644 index 00000000000..6c5e2f251a1 --- /dev/null +++ b/tool-data/mosaik_index.loc.sample @@ -0,0 +1,19 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Mosaik indexed sequences data files. You will need +#to create these data files and then create a mosaik_index.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The mosaik_index.loc +#file has this format (longer white space is the TAB character): +# +# +# +#So, for example, if you had hg18 indexed and stored in +#/depot/data2/galaxy/mosaik/hg18/ +#then the mosaik_index.loc entry would look like this: +# +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/mosaik/hg18/hg18.fa +# +#and your /depot/data2/galaxy/mosaik/hg18/ directory +#would contain the following files: +#TODO handle mosaik jump tables. +# diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample index ef39c53463b..0a9ac625a57 100644 --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -291,6 +291,7 @@ +
@@ -369,6 +370,7 @@ +
diff --git a/tool_data_table_conf.xml.sample b/tool_data_table_conf.xml.sample index 2ddeb064b62..7c7c9e5913b 100644 --- a/tool_data_table_conf.xml.sample +++ b/tool_data_table_conf.xml.sample @@ -80,4 +80,9 @@ value, name, path + + + value, dbkey, name, path + +
diff --git a/tools/human_genome_variation/freebayes.xml b/tools/human_genome_variation/freebayes.xml new file mode 100644 index 00000000000..5e22df9f249 --- /dev/null +++ b/tools/human_genome_variation/freebayes.xml @@ -0,0 +1,116 @@ + + + + freebayes + + Bayesian genetic variant detector + + freebayes --fasta-reference $reference $bamfile --vcf $output + #if $params.source_select == "full": + $params.showRefRepeats + -T $params.theta + -p $params.ploidy + $params.pooled + $params.mnps + $params.nosnps + -n $params.bestAlleles + $params.allAlleles + $params.duplicateReads + -M $params.refMapQuality + $params.ignoreRefAllele + $params.haploidReference + -m $params.minMapQuality + -q $params.minBaseQuality + $params.noFilters + -x $params.indelExclusionWindow + + -V $params.diffusionPriorScalar + -W $params.postIntegBandwidth + -Y $params.postIntegBanddepth + -F $params.minAltFraction + -C $params.minAltCount + -G $params.minAltTotal + --min-coverage $params.minCoverage + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +This tool uses Freebayes to call SNPS given a reference sequence and a BAM alignment file. + + diff --git a/tools/sr_mapping/mosaik.xml b/tools/sr_mapping/mosaik.xml new file mode 100644 index 00000000000..bd914ccab69 --- /dev/null +++ b/tools/sr_mapping/mosaik.xml @@ -0,0 +1,93 @@ + + + + mosaik + + #set $processors = '-p 4' + #set $lm = '' + #if $paired.kind == 'single': + #set $mfl = '' + #set $ls = '' + #else: + #set $ls = '-ls $mfl' + #end if + MosaikBuild -fr + #if $genomeSource.refGenomeSource == 'indexed': + ##$genomeSource.indexReference + ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] } + #else: + $genomeSource.historyReference + #end if + -oa mosaik_ref_file; + MosaikBuild -q $reads $mfl -st $st -out mosaik_reads_file; + MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls -mm $mm -mhp $mhp -act $act -bw $bw $processors $lm -hs 15; + MosaikText -in mosaik_aligned_file -$outFormat sam_bam_file; + #if str($outFormat) == 'bam': + samtools sort sam_bam_file sorted_bam; + mv sorted_bam.bam $output + #else: + gunzip sam_bam_file.gz; + mv sam_bam_file $output + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +This tool uses Mosaik to align reads to a reference sequence. + +