# HG changeset patch
# User iuc
# Date 1485169625 18000
# Node ID edaa8572219dd45b96aa8114b8077f5be952d5c1
# Parent  89c9361b93daf61b4addc40114ef0879f80a10a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit a8611c912a8265de6f64a3e17cea63c87fa48b8e

diff -r 89c9361b93da -r edaa8572219d sickle.xml
--- a/sickle.xml	Sat Jan 21 13:08:43 2017 -0500
+++ b/sickle.xml	Mon Jan 23 06:07:05 2017 -0500
@@ -12,12 +12,12 @@
         #if str($readtype.single_or_paired) == "se":
             se -f "${readtype.input_single}" -o "$output_single"
 
-            #if $readtype.is_of_type("fastq", "fastqsanger"):
-                -t sanger
-            #else if $readtype.input_single.is_of_type('fastqillumina'):
+            #if $readtype.input_single.is_of_type('fastqillumina'):
                 -t illumina
             #else if $readtype.input_single.is_of_type('fastqsolexa'):
                 -t solexa
+            #else:
+                -t sanger
             #end if
         #end if
 
@@ -28,36 +28,36 @@
                 pe -c "${readtype.input_combo}" -m "$output_combo" -s "$output_combo_single"
             #end if
 
-            #if $readtype.input_combo.is_of_type("fastq", "fastqsanger"):
-                -t sanger
-            #else if $readtype.input_combo.is_of_type('fastqillumina'):
+            #if $readtype.input_combo.is_of_type('fastqillumina'):
                 -t illumina
             #else if $readtype.input_combo.is_of_type('fastqsolexa'):
                 -t solexa
+            #else:
+                -t sanger
             #end if
         #end if
 
         #if str($readtype.single_or_paired) == "pe_sep":
             pe -f "${readtype.input_paired1}" -r "${readtype.input_paired2}" -o "$output_paired1" -p "$output_paired2" -s "$output_paired_single"
 
-            #if $readtype.input_paired1.is_of_type("fastq", "fastqsanger"):
-                -t sanger
-            #else if $readtype.input_paired1.is_of_type('fastqillumina'):
+            #if $readtype.input_paired1.is_of_type('fastqillumina'):
                 -t illumina
             #else if $readtype.input_paired1.is_of_type('fastqsolexa'):
                 -t solexa
+            #else:
+                -t sanger
             #end if
         #end if
 
         #if str($readtype.single_or_paired) == "pe_collection":
             pe -f "${readtype.input_paired.forward}" -r "${readtype.input_paired.reverse}" -o "${output_paired_coll.forward}" -p "${output_paired_coll.reverse}" -s "$output_paired_coll_single"
 
-            #if $readtype.input_paired.forward.is_of_type("fastq", "fastqsanger"):
-                -t sanger
-            #else if $readtype.input_paired.forward.is_of_type('fastqillumina'):
+            #if $readtype.input_paired.forward.is_of_type('fastqillumina'):
                 -t illumina
             #else if $readtype.input_paired.forward.is_of_type('fastqsolexa'):
                 -t solexa
+            #else:
+                -t sanger
             #end if
         #end if