Mercurial > repos > iuc > umi_tools_whitelist

changeset 3:853f74e08009 draft

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planemo upload commit d8f6e961cc9f14c5b39762f87e11352c0aadefc9
author iuc
date Sat, 31 Mar 2018 17:36:28 -0400
parents c1743022a8cd
children 095c349b4343
files umi-tools_whitelist.xml
diffstat 1 files changed, 12 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/umi-tools_whitelist.xml	Thu Mar 29 18:24:04 2018 -0400
+++ b/umi-tools_whitelist.xml	Sat Mar 31 17:36:28 2018 -0400
@@ -25,20 +25,29 @@
             #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):
                 ln -s '$input_type.input_single' input_single.gz &&
                 #set $gz = True
+            #else
+                ln -s '$input_type.input_single' input_single.txt &&
             #end if
         #elif $input_type.type == 'paired':
             #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
                 ln -s '$input_type.input_read1' input_read1.gz &&
                 ln -s '$input_type.input_read2' input_read2.gz &&
                 #set $gz = True
+            #else
+                ln -s '$input_type.input_read1' input_read1.txt &&
+                ln -s '$input_type.input_read2' input_read2.txt &&
             #end if
         #else  ## paired_collection
             #if $input_type.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
                 ln -s '$input_type.input_readpair.forward' input_read1.gz &&
                 ln -s '$input_type.input_readpair.reverse' input_read2.gz &&
                 #set $gz = True
+            #else
+                ln -s '$input_type.input_readpair.forward' input_read1.txt &&
+                ln -s '$input_type.input_readpair.reverse' input_read2.txt &&
             #end if
         #end if
+
         umi_tools whitelist
             --bc-pattern='$bc_pattern'
             --subset-reads='$subset_reads'
@@ -46,15 +55,15 @@
                 #if $gz:
                     --stdin=input_single.gz
                 #else
-                    --stdin='$input_type.input_single'
+                    --stdin=input_single.txt
                 #end if
             #else:  ## equally valid for both 'paired' and 'paired_collection'
                 #if $gz:
                     --stdin=input_read1.gz
                     --read2-in=input_read2.gz
                 #else:
-                    --stdin='$input_type.input_read1'
-                    --read2-in='$input_type.input_read2'
+                    --stdin=input_read1.txt
+                    --read2-in=input_read2.txt
                 #end if
                 #if $input_type.barcode.barcode_select == "1":
                     --bc-pattern2='$input_type.barcode.bc_pattern2'