# HG changeset patch # User degregory # Date 1631542460 0 # Node ID b68f7e37e70a7551b47aa46ecda071f9fe7b3f1b # Parent 22e3f843f1db0544d86aa899049b91bbbccff4a5 Uploaded xml diff -r 22e3f843f1db -r b68f7e37e70a SAM_Refiner_Gal.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SAM_Refiner_Gal.xml Mon Sep 13 14:14:20 2021 +0000 @@ -0,0 +1,120 @@ + + Provides variant information from mapped reads + + python '${__tool_directory__}/SAM_Refiner_Gal.py' -r $ref -S $samfile --min_samp_abund $minsampabund --min_count $mincount --ntabund $ntab --max_dist $maxdist --max_covar $maxcov +#if $use_count + --use_count 1 +#else + --use_count 0 +#end if +#if $seqs + -o1 $out_file1 +#else + --seq 0 +#end if +#if $indels + -o2 $out_file2 +#else + --indel 0 +#end if +#if $ntcalls: + -o3 $out_file3 +#else + --nt_call 0 +#end if +#if $covars + -o4 $out_file4 +#else + --covar 0 +#end if +#if $chimrm + -o5 $out_file5 --alpha $alpha --foldab $foldab +#else + --chim_rm 0 +#end if +#if $covdec + -o6 $out_file6 --beta $beta --autopass $pass +#else + --deconv 0 +#end if +#if $ntvar + --ntvar 1 + -o7 $out_file7 +#end if +#if $AArep + --AAreport 1 +#else + --AAreport 0 +#end if +#if $MNP + --AAcodonasMNP 1 +#else + --AAcodonasMNP 0 +#end if +#if $redist + --redist 1 +#else + --redist 0 +#end if + --samp '$samp' +#if $WGS + --wgs 1 +#else + --wgs 0 +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +SAM Refiner provides variant information from mapped reads in a SAM file. If you use this tool, please reference Gregory, D.A.; Wieberg, C.G.; Wenzel, J.; Lin, C.-H.; Johnson, M.C. Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. Viruses 2021, 13, 1647. https://doi.org/10.3390/v13081647 + + + + + \ No newline at end of file