# HG changeset patch
# User iuc
# Date 1554745762 14400
# Node ID e4691e1589d3c466672ce19de71c5324a25a3e23
# Parent  49370cb85f0ff8a78499dbffdad32451292e7263
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8

diff -r 49370cb85f0f -r e4691e1589d3 cutadapt.xml
--- a/cutadapt.xml	Tue Dec 18 14:09:53 2018 -0500
+++ b/cutadapt.xml	Mon Apr 08 13:49:22 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="cutadapt" name="Cutadapt" version="1.16.5" profile="17.09">
+<tool id="cutadapt" name="Cutadapt" version="1.16.6" profile="17.09">
     <description>Remove adapter sequences from Fastq/Fasta</description>
     <macros>
         <import>macros.xml</import>
@@ -35,34 +35,38 @@
 #end if
 
 #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
-    #set read1 = $read1 + ".fq.gz"
-    #set out1 = "out1.gz"
+    #set ext = ".fq.gz"
 #else if $input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-    #set read1 = $read1 + ".fq.bz2"
-    #set out1 = "out1.bz2"
+    #set ext = ".fq.bz2"
 #else if $input_1.is_of_type('fasta'):
-    #set read1 = $read1 + ".fa"
-    #set out1 = "out1.fa"
+    #set ext = ".fa"
 #else:
-    #set read1 = $read1 + ".fq"
-    #set out1 = "out1.fq"
+    #set ext = ".fq"
 #end if
+#set read1 = $read1 + $ext
+#set out1 = "out1" + $ext
+#set rest_output = "rest_output" + $ext
+#set wild_output = "wild_output" + $ext
+#set too_short_output = "too_short_output" + $ext
+#set too_long_output = "too_long_output" + $ext
+#set untrimmed_output = "untrimmed_output" + $ext
 ln -f -s '${input_1}' '$read1' &&
 
 #if $paired:
     #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
-        #set read2 = $read2 + ".fq.gz"
-        #set out2 = "out2.gz"
+        #set ext2 = ".fq.gz"
     #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-        #set read2 = $read2 + ".fq.bz2"
-        #set out2 = "out2.bz2"
+        #set ext2 = ".fq.gz"
     #else if $input_2.is_of_type('fasta'):
-        #set read2 = $read2 + ".fa"
-        #set out2 = "out2.fa"
+        #set ext2 = ".fa"
     #else:
-        #set read2 = $read2 + ".fq"
-        #set out2 = "out2.fq"
+        #set ext2 = ".fq"
     #end if
+    #set read2 = $read2 + $ext2
+    #set out2 = "out2" + $ext2
+    #set too_short_paired_output = "too_short_paired_output" + $ext2
+    #set too_long_paired_output = "too_long_paired_output" + $ext2
+    #set untrimmed_paired_output = "untrimmed_paired_output" + $ext2
     ln -f -s '${input_2}' '$read2' &&
 #end if
 
@@ -252,40 +256,40 @@
             <filter>(output_options['info_file'] is True)</filter>
         </data>
 
-        <data name="rest_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" >
+        <data name="rest_output" format="fastqsanger" metadata_source="input_1" from_work_dir="rest_output*" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" >
             <filter>(output_options['rest_file'] is True)</filter>
             <expand macro="inherit_format_1" />
         </data>
 
-        <data name="wild_output" format="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Wildcard File" >
+        <data name="wild_output" format="txt" metadata_source="input_1" from_work_dir="wild_output*" label="${tool.name} on ${on_string}: Wildcard File" >
             <filter>(output_options['wildcard_file'] is True)</filter>
         </data>
 
-        <data name="untrimmed_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Untrimmed Read 1" >
+        <data name="untrimmed_output" format="fastqsanger" metadata_source="input_1" from_work_dir="untrimmed_output*" label="${tool.name} on ${on_string}: Untrimmed Read 1" >
             <filter>(output_options['untrimmed_file'] is True)</filter>
             <expand macro="inherit_format_1" />
         </data>
-        <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="input_2" label="${tool.name} on ${on_string}: Untrimmed Read 2" >
+        <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="untrimmed_paired_output*" label="${tool.name} on ${on_string}: Untrimmed Read 2" >
             <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
             <filter>(output_options['untrimmed_file'] is True)</filter>
             <expand macro="inherit_format_2" />
         </data>
 
-        <data name="too_short_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Too Short Read 1" >
+        <data name="too_short_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_short_output*" label="${tool.name} on ${on_string}: Too Short Read 1" >
             <filter>(output_options['too_short_file'] is True)</filter>
             <expand macro="inherit_format_1" />
         </data>
-        <data name="too_short_paired_output" format="fastqsanger" metadata_source="input_2" label="${tool.name} on ${on_string}: Too Short Read 2" >
+        <data name="too_short_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_short_paired_output*" label="${tool.name} on ${on_string}: Too Short Read 2" >
             <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
             <filter>(output_options['too_short_file'] is True)</filter>
             <expand macro="inherit_format_2" />
         </data>
 
-        <data name="too_long_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Too Long Read 1" >
+        <data name="too_long_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_long_output*" label="${tool.name} on ${on_string}: Too Long Read 1" >
             <filter>(output_options['too_long_file'] is True)</filter>
             <expand macro="inherit_format_1" />
         </data>
-        <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" label="${tool.name} on ${on_string}: Too Long Read 2" >
+        <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" >
             <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
             <filter>(output_options['too_long_file'] is True)</filter>
             <expand macro="inherit_format_2" />
@@ -463,6 +467,32 @@
                  </output_collection>
             </test>
 
+        <!-- Ensure untrimmed file output works -->
+        <test>
+            <param name="type" value="single" />
+            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
+            <param name="adapter_source_list" value="user"/>
+            <param name="adapter" value="AAAT"/>
+            <param name="untrimmed_file" value="True" />
+            <output name="out1" file="cutadapt_trimmed.out" ftype="fastq"/>
+            <output name="untrimmed_output" file="cutadapt_untrimmed.out" ftype="fastq"/>
+        </test>
+        <!-- Ensure untrimmed gzip file output works -->
+        <test>
+            <param name="type" value="single" />
+            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
+            <param name="adapter_source_list" value="user"/>
+            <param name="adapter" value="AGATCGGAAGAGC"/>
+            <param name="untrimmed_file" value="True" />
+            <output name="out1" decompress="True" file="cutadapt_trimmed.out.gz" ftype="fastq.gz"/>
+            <!-- 
+                Do not use the decompress option for this assertion, since it does NOT test that the file is compressed
+                See discussion at https://github.com/galaxyproject/galaxy/issues/7671
+                `delta="4000" is more than the difference between gzip level 1 and gzip level 9, but much less than the
+                difference between level 1 compression and no compression
+            -->
+            <output name="untrimmed_output" file="cutadapt_untrimmed.out.gz" compare="sim_size" delta="4000" ftype="fastq.gz"/>
+        </test>
     </tests>
 
     <help><![CDATA[
diff -r 49370cb85f0f -r e4691e1589d3 macros.xml
--- a/macros.xml	Tue Dec 18 14:09:53 2018 -0500
+++ b/macros.xml	Mon Apr 08 13:49:22 2019 -0400
@@ -48,19 +48,19 @@
             --info-file=$info_file
         #end if
         #if $output_options.rest_file:
-            --rest-file=$rest_output
+            --rest-file='${rest_output}'
         #end if
         #if $output_options.wildcard_file:
-            --wildcard-file=$wild_output
+            --wildcard-file='${wild_output}'
         #end if
         #if $output_options.too_short_file:
-            --too-short-output=$too_short_output
+            --too-short-output='${too_short_output}'
         #end if
         #if $output_options.too_long_file:
-            --too-long-output=$too_long_output
+            --too-long-output='${too_long_output}'
         #end if
         #if $output_options.untrimmed_file:
-            --untrimmed-output=$untrimmed_output
+            --untrimmed-output='${untrimmed_output}'
         #end if
 
     ]]></token>
@@ -110,13 +110,13 @@
         ## Additional Outputs - Read 2
 
         #if $output_options.too_short_file:
-            --too-short-paired-output=$too_short_paired_output
+            --too-short-paired-output='${too_short_paired_output}'
         #end if
         #if $output_options.too_long_file:
-            --too-long-paired-output=$too_long_paired_output
+            --too-long-paired-output='${too_long_paired_output}'
         #end if
         #if $output_options.untrimmed_file:
-            --untrimmed-paired-output=$untrimmed_paired_output
+            --untrimmed-paired-output='${untrimmed_paired_output}'
         #end if
 
     ]]></token>
diff -r 49370cb85f0f -r e4691e1589d3 test-data/cutadapt_trimmed.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cutadapt_trimmed.out	Mon Apr 08 13:49:22 2019 -0400
@@ -0,0 +1,4 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGAC
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77
diff -r 49370cb85f0f -r e4691e1589d3 test-data/cutadapt_trimmed.out.gz
Binary file test-data/cutadapt_trimmed.out.gz has changed
diff -r 49370cb85f0f -r e4691e1589d3 test-data/cutadapt_untrimmed.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cutadapt_untrimmed.out	Mon Apr 08 13:49:22 2019 -0400
@@ -0,0 +1,8 @@
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:
diff -r 49370cb85f0f -r e4691e1589d3 test-data/cutadapt_untrimmed.out.gz
Binary file test-data/cutadapt_untrimmed.out.gz has changed