Mercurial > repos > devteam > bowtie2
changeset 6:e23b0cdeeba6 draft
planemo upload commit 5ad726dc73203a704666033cd3bf70b82575978f
| author | devteam |
|---|---|
| date | Wed, 26 Aug 2015 12:46:11 -0400 |
| parents | 42bb952b4e3c |
| children | 4f92dccc808a |
| files | bowtie2_wrapper.xml read_group_macros.xml |
| diffstat | 2 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/bowtie2_wrapper.xml Tue Jul 21 13:01:59 2015 -0400 +++ b/bowtie2_wrapper.xml Wed Aug 26 12:46:11 2015 -0400 @@ -76,11 +76,11 @@ ## Read group information. @define_read_group_helpers@ #if str( $library.type ) == "single": - #set $rg_auto_name = $read_group_name_default($library.input_1) + #set $rg_auto_name = $read_group_name_default($library.input_1) #elif str( $library.type ) == "paired": - #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2) + #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2) #else - #set $rg_auto_name = $read_group_name_default($library.input_1) + #set $rg_auto_name = $read_group_name_default($library.input_1) #end if @set_use_rg_var@ @set_read_group_vars@
--- a/read_group_macros.xml Tue Jul 21 13:01:59 2015 -0400 +++ b/read_group_macros.xml Wed Aug 26 12:46:11 2015 -0400 @@ -2,7 +2,6 @@ <!-- Import this at the top of your command block and then define rg_auto_name. --> <token name="@define_read_group_helpers@"> -#import re #def identifier_or_name($input1) #if hasattr($input1, 'element_identifier') #return $input1.element_identifier @@ -12,6 +11,7 @@ #end def #def clean(name) + #import re #set $name_clean = re.sub('[^\w\-_\.]', '_', $name) #return $name_clean #end def @@ -79,7 +79,7 @@ #if $rg_param('read_group_lb_conditional') is None #set $rg_lb = '' - #elif $rg_param('read_group_lb_conditional')do_auto_name + #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) @@ -147,7 +147,7 @@ </xml> <xml name="read_group_id_param"> <param name="ID" type="text" value="" size="20" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false"> - <validator type="empty_field" /> + <validator type="empty_field" /> </param> </xml> <xml name="read_group_id_conditional">