# HG changeset patch # User scisjnu123 # Date 1568356506 14400 # Node ID 050856988602658988d1e8760feec12f8638be81 # Parent 24d2dc34dd17c29953a7cff53d2bd8ee39a6cc99 Uploaded diff -r 24d2dc34dd17 -r 050856988602 picard/read_group_macros.xml --- a/picard/read_group_macros.xml Fri Sep 13 02:21:23 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,294 +0,0 @@ - - - -#def identifier_or_name($input1) - #if hasattr($input1, 'element_identifier') - #return $input1.element_identifier - #else - #return $input1.name.rstrip('.gz').rstrip('.fastq').rstrip('.fq') - #end if -#end def - -#def clean(name) - #import re - #set $name_clean = re.sub('[^\w\-_\.]', '_', $name) - #return $name_clean -#end def - -#def read_group_name_default($input1, $input2=None) - #if $input2 is None - #return $clean($identifier_or_name($input1)) - #else - #import itertools - #set $input_name1 = $clean($identifier_or_name($input1)) - #set $input_name2 = $clean($identifier_or_name($input2)) - #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), itertools.izip(*[$input_name1, $input_name2]))]) - #if len($common_prefix) > 3 - #return $common_prefix - #else - #return $input_name1 - #end if - #end if -#end def - -#def format_read_group(prefix, value, quote='', arg='') - #if $value - #return $arg + $quote + $prefix + $value + $quote - #else - #return '' - #end if -#end def - -#def rg_param(name) - #if $varExists("rg") - #return $rg.get($name, None) - #else - #return $getVar($name, None) - #end if -#end def - -#set $use_rg = True - - - -#if $use_rg - #if $rg_param('read_group_id_conditional') is None - #set $rg_id = $rg_auto_name - #elif $rg_param('read_group_id_conditional').do_auto_name - #set $rg_id = $rg_auto_name - #else - #set $rg_id = str($rg_param('read_group_id_conditional').ID) - #end if - - #if $rg_param('read_group_sm_conditional') is None - #set $rg_sm = '' - #elif $rg_param('read_group_sm_conditional').do_auto_name - #set $rg_sm = $rg_auto_name - #else - #set $rg_sm = str($rg_param('read_group_sm_conditional').SM) - #end if - - #if $rg_param('PL') - #set $rg_pl = str($rg_param('PL')) - #else - #set $rg_pl = '' - #end if - - #if $rg_param('read_group_lb_conditional') is None - #set $rg_lb = '' - #elif $rg_param('read_group_lb_conditional').do_auto_name - #set $rg_lb = $rg_auto_name - #else - #set $rg_lb = str($rg_param('read_group_lb_conditional').LB) - #end if - - #if $rg_param('CN') - #set $rg_cn = str($rg_param('CN')) - #else - #set $rg_cn = '' - #end if - - #if $rg_param("DS") - #set $rg_ds = str($rg_param("DS")) - #else - #set $rg_ds = '' - #end if - - #if $rg_param("DT") - #set $rg_dt = str($rg_param("DT")) - #else - #set $rg_dt = '' - #end if - - #if $rg_param("FO") - #set $rg_fo = str($rg_param("FO")) - #else - #set $rg_fo = '' - #end if - - #if $rg_param("KS") - #set $rg_ks = str($rg_param("KS")) - #else - #set $rg_ks = '' - #end if - - #if $rg_param("PG") - #set $rg_pg = str($rg_param("PG")) - #else - #set $rg_pg = '' - #end if - - #if str($rg_param("PI")) - #set $rg_pi = str($rg_param("PI")) - #else - #set $rg_pi = '' - #end if - - #if $rg_param("PU") - #set $rg_pu = str($rg_param("PU")) - #else - #set $rg_pu = '' - #end if -#end if - - -#set $use_rg = str($rg.rg_selector) != "do_not_set" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \*|[ACMGRSVTWYHKDBN]+$ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -