diff cutadapt.xml @ 22:093678460093 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"

--- a/cutadapt.xml	Thu Mar 05 06:45:31 2020 -0500
+++ b/cutadapt.xml	Sat Jul 04 06:52:59 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="cutadapt" name="Cutadapt" version="1.16.7" profile="17.09">
+<tool id="cutadapt" name="Cutadapt" version="1.16.8" profile="17.09">
     <description>Remove adapter sequences from Fastq/Fasta</description>
     <macros>
         <import>macros.xml</import>
@@ -113,7 +113,7 @@
 #if str($filter_options.max):
     --maximum-length=$filter_options.max
 #end if
-#if $filter_options.max_n:
+#if str($filter_options.max_n):
     --max-n=$filter_options.max_n
 #end if
 #if str( $library.type ) != "single":
@@ -131,16 +131,16 @@
 #end if
 $read_mod_options.trim_n
 #if $read_mod_options.prefix != '':
-    --prefix="$read_mod_options.prefix"
+    --prefix='$read_mod_options.prefix'
 #end if
 #if $read_mod_options.suffix != '':
-    --suffix="$read_mod_options.suffix"
+    --suffix='$read_mod_options.suffix'
 #end if
 #if str($read_mod_options.length) != '0':
     --length=$read_mod_options.length
 #end if
 #if $read_mod_options.length_tag != '':
-    --length-tag="$read_mod_options.length_tag"
+    --length-tag='$read_mod_options.length_tag'
 #end if
 
 '${read1}'
@@ -518,14 +518,14 @@
                 <param name="discard_untrimmed" value="true"/>
                 <param name="min" value="1"/>
                 <param name="max" value="1000"/>
-                <param name="max_n" value="1"/>
+                <param name="max_n" value="0"/>
                 <param name="pair_filter" value="both"/>
             </section>
             <assert_command>
                 <has_text text="--discard-untrimmed"/>
                 <has_text text="--minimum-length=1"/>
                 <has_text text="--maximum-length=1000"/>
-                <has_text text="--max-n=1"/>
+                <has_text text="--max-n=0"/>
                 <has_text text="--pair-filter=both"/>
             </assert_command>
         </test>