# HG changeset patch
# User iuc
# Date 1485022123 18000
# Node ID 89c9361b93daf61b4addc40114ef0879f80a10a7
# Parent  01327506044335b25ac625a74c97e1b3f1f59fcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7fded35b9fb8ba9ebfb4b4ab44f39bb51e9bc125

diff -r 013275060443 -r 89c9361b93da sickle.xml
--- a/sickle.xml	Wed Nov 09 05:54:27 2016 -0500
+++ b/sickle.xml	Sat Jan 21 13:08:43 2017 -0500
@@ -12,11 +12,11 @@
         #if str($readtype.single_or_paired) == "se":
             se -f "${readtype.input_single}" -o "$output_single"
 
-            #if $readtype.input_single.ext in ("fastq", "fastqsanger"):
+            #if $readtype.is_of_type("fastq", "fastqsanger"):
                 -t sanger
-            #else if $readtype.input_single.ext == "fastqillumina":
+            #else if $readtype.input_single.is_of_type('fastqillumina'):
                 -t illumina
-            #else if $readtype.input_single.ext == "fastqsolexa":
+            #else if $readtype.input_single.is_of_type('fastqsolexa'):
                 -t solexa
             #end if
         #end if
@@ -28,11 +28,11 @@
                 pe -c "${readtype.input_combo}" -m "$output_combo" -s "$output_combo_single"
             #end if
 
-            #if $readtype.input_combo.ext in ("fastq", "fastqsanger"):
+            #if $readtype.input_combo.is_of_type("fastq", "fastqsanger"):
                 -t sanger
-            #else if $readtype.input_combo.ext == "fastqillumina":
+            #else if $readtype.input_combo.is_of_type('fastqillumina'):
                 -t illumina
-            #else if $readtype.input_combo.ext == "fastqsolexa":
+            #else if $readtype.input_combo.is_of_type('fastqsolexa'):
                 -t solexa
             #end if
         #end if
@@ -40,11 +40,11 @@
         #if str($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.ext in ("fastq", "fastqsanger"):
+            #if $readtype.input_paired1.is_of_type("fastq", "fastqsanger"):
                 -t sanger
-            #else if $readtype.input_paired1.ext == "fastqillumina":
+            #else if $readtype.input_paired1.is_of_type('fastqillumina'):
                 -t illumina
-            #else if $readtype.input_paired1.ext == "fastqsolexa":
+            #else if $readtype.input_paired1.is_of_type('fastqsolexa'):
                 -t solexa
             #end if
         #end if
@@ -52,11 +52,11 @@
         #if str($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.ext in ("fastq", "fastqsanger"):
+            #if $readtype.input_paired.forward.is_of_type("fastq", "fastqsanger"):
                 -t sanger
-            #else if $readtype.input_paired.forward.ext == "fastqillumina":
+            #else if $readtype.input_paired.forward.is_of_type('fastqillumina'):
                 -t illumina
-            #else if $readtype.input_paired.forward.ext == "fastqsolexa":
+            #else if $readtype.input_paired.forward.is_of_type('fastqsolexa'):
                 -t solexa
             #end if
         #end if
diff -r 013275060443 -r 89c9361b93da tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 09 05:54:27 2016 -0500
+++ b/tool_dependencies.xml	Sat Jan 21 13:08:43 2017 -0500
@@ -1,14 +1,14 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="zlib" version="1.2.8">
-        <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="411985b46ae8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="sickle" version="1.33">
         <install version="1.0">
             <actions>
                 <action target_filename="sickle-1.33.tar.gz" type="download_by_url">https://github.com/najoshi/sickle/archive/v1.33.tar.gz</action>
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="411985b46ae8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                         <package name="zlib" version="1.2.8" />
                     </repository>
                 </action>