# HG changeset patch
# User iuc
# Date 1554335360 14400
# Node ID a27654fc427003c33af99b406a50a3b3e8716061
# Parent  c85bdba47254a65d7b4bfd4717ecb2c6a98f82af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31

diff -r c85bdba47254 -r a27654fc4270 flash.xml
--- a/flash.xml	Mon Apr 01 19:01:31 2019 -0400
+++ b/flash.xml	Wed Apr 03 19:49:20 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="flash" name="FLASH" version="@VERSION@.3">
+<tool id="flash" name="FLASH" version="@VERSION@.4">
     <description>adjust length of short reads</description>
     <macros>
         <token name="@VERSION@">1.2.11</token>
@@ -22,12 +22,15 @@
                     '$layout.reads.forward' '$layout.reads.reverse'
                     #set $input = $layout.reads.forward
                 #end if
-                #if $input.is_of_type('fastqsanger'):
+                #if $input.is_of_type('fastqsanger', 'fastqsanger.gz'):
                     -p 33
                 #else:
                     -p 64
                 #end if
-
+                #if $input.ext.endswith('.gz'):
+                    -z
+                #end if
+                --output-suffix=''
                 #if $save_log:
                     > '$log'
                 #end if
@@ -40,11 +43,11 @@
                 <option value="collection">Paired collection</option>
             </param>
             <when value="individual">
-                <param format="fastqsanger,fastqsolexa,fastqillumina" name="forward" type="data" label="Forward reads" />
-                <param format="fastqsanger,fastqsolexa,fastqillumina" name="reverse" type="data" label="Reverse reads" />
+                <param format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" name="forward" type="data" label="Forward reads" />
+                <param format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" name="reverse" type="data" label="Reverse reads" />
             </when>
             <when value="collection">
-                <param format="fastqsanger,fastqsolexa,fastqillumina" name="reads" type="data_collection" collection_type="paired" label="Paired reads" />
+                <param format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" name="reads" type="data_collection" collection_type="paired" label="Paired reads" />
             </when>
         </conditional>
         <param name="min_overlap" argument="--min-overlap" type="integer" optional="true" value="10" label="Minimum overlap" help="The minimum required overlap length between two reads to provide a confident overlap." />
@@ -146,6 +149,35 @@
             <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" />
             <output name="hist" file="flash_hist_out3.tabular" />
         </test>
+        <test>
+            <param name="select_layout" value="individual" />
+            <param name="forward" value="flash_forward_in4.fastqsanger.gz" ftype="fastqsanger.gz" />
+            <param name="reverse" value="flash_reverse_in4.fastqsanger.gz" ftype="fastqsanger.gz" />
+            <param name="generate_histogram" value="false" />
+            <param name="save_log" value="true" />
+            <output name="merged_paired_reads" file="flash_merged_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
+            <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
+            <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
+            <output name="log">
+              <assert_contents>
+                <has_line_matching expression=".*Percent combined: 3.60%" />
+              </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="select_layout" value="collection" />
+            <param name="generate_histogram" value="false" />
+            <param name="reads">
+                <collection type="paired">
+                    <element name="forward" value="flash_forward_in5.fastqsanger.gz" ftype="fastqsanger.gz" />
+                    <element name="reverse" value="flash_reverse_in5.fastqsanger.gz" ftype="fastqsanger.gz" />
+                </collection>
+            </param>
+            <output name="merged_reads" file="flash_merged_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
+            <output name="unmerged_reads_f" file="flash_unmerged_f_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
+            <output name="unmerged_reads_r" file="flash_unmerged_r_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
+            <output name="hist" file="flash_hist_out5.tabular" />
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r c85bdba47254 -r a27654fc4270 test-data/flash_forward_in4.fastqsanger.gz
Binary file test-data/flash_forward_in4.fastqsanger.gz has changed
diff -r c85bdba47254 -r a27654fc4270 test-data/flash_forward_in5.fastqsanger.gz
Binary file test-data/flash_forward_in5.fastqsanger.gz has changed
diff -r c85bdba47254 -r a27654fc4270 test-data/flash_hist_out5.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_hist_out5.tabular	Wed Apr 03 19:49:20 2019 -0400
@@ -0,0 +1,14 @@
+352	1
+367	1
+368	2
+370	1
+374	1
+375	1
+376	2
+377	1
+379	1
+382	1
+383	1
+385	1
+386	1
+388	3
diff -r c85bdba47254 -r a27654fc4270 test-data/flash_merged_out4.fastqsanger.gz
Binary file test-data/flash_merged_out4.fastqsanger.gz has changed
diff -r c85bdba47254 -r a27654fc4270 test-data/flash_merged_out5.fastqsanger.gz
Binary file test-data/flash_merged_out5.fastqsanger.gz has changed
diff -r c85bdba47254 -r a27654fc4270 test-data/flash_reverse_in4.fastqsanger.gz
Binary file test-data/flash_reverse_in4.fastqsanger.gz has changed
diff -r c85bdba47254 -r a27654fc4270 test-data/flash_reverse_in5.fastqsanger.gz
Binary file test-data/flash_reverse_in5.fastqsanger.gz has changed
diff -r c85bdba47254 -r a27654fc4270 test-data/flash_unmerged_f_out4.fastqsanger.gz
Binary file test-data/flash_unmerged_f_out4.fastqsanger.gz has changed
diff -r c85bdba47254 -r a27654fc4270 test-data/flash_unmerged_f_out5.fastqsanger.gz
Binary file test-data/flash_unmerged_f_out5.fastqsanger.gz has changed
diff -r c85bdba47254 -r a27654fc4270 test-data/flash_unmerged_r_out4.fastqsanger.gz
Binary file test-data/flash_unmerged_r_out4.fastqsanger.gz has changed
diff -r c85bdba47254 -r a27654fc4270 test-data/flash_unmerged_r_out5.fastqsanger.gz
Binary file test-data/flash_unmerged_r_out5.fastqsanger.gz has changed