Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 32:2b6a44353622
Uploaded
| author | yhoogstrate |
|---|---|
| date | Mon, 17 Feb 2014 10:47:38 -0500 |
| parents | af8a55f9dcc0 |
| children | 3f62f407068e |
| files | varscan_mpileup2snp_from_bam.xml |
| diffstat | 1 files changed, 3 insertions(+), 7 deletions(-) [+] |
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--- a/varscan_mpileup2snp_from_bam.xml Mon Feb 17 10:42:46 2014 -0500 +++ b/varscan_mpileup2snp_from_bam.xml Mon Feb 17 10:47:38 2014 -0500 @@ -10,6 +10,7 @@ echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2 #else + <!-- Development stuff - might be useful for later #if $reference_genome_source.source_select == "indexed_filtered" echo "USED FASTA = $reference_genome_source.reference_genome" #else if $reference_genome_source.source_select == "indexed_all" @@ -17,16 +18,11 @@ #else if $reference_genome_source.source_select == "history" echo "USED FASTA = $reference_genome_source.reference_genome" #else - <!-- - This is a workaround to obtain the "genome.fa" file that - corresponds to the dbkey of the alignments. - Because this file is "calculated" during run-time, it can - be used in a workflow. - --> echo "USED FASTA = ${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" #end if ; + --> samtools-mpileup-parallel mpileup -t $samtools_threads @@ -109,7 +105,7 @@ <!-- Find out how to access the reference genome from the BAM file(s) --> <conditional name="reference_genome_source"> <param name="source_select" type="select" label="Fasta Source"> - <option value="indexed_filtered">Use a built-in index (which fit your reference)</option> + <option value="indexed_filtered">Use a built-in index (which fits your reference)</option> <option value="history">Use reference from the history</option> <option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option> <option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option>