# HG changeset patch
# User artbio
# Date 1562680336 14400
# Node ID 55cf9d9defd1e0e8ac111e678908944bc6fa2711
# Parent  4554fa330d3d7e3a7c6dd132f06f4fb3fa78e6df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f

diff -r 4554fa330d3d -r 55cf9d9defd1 catWrapper.xml
--- a/catWrapper.xml	Mon Jun 24 04:02:53 2019 -0400
+++ b/catWrapper.xml	Tue Jul 09 09:52:16 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.4.0">
+<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.4.1">
     <description>tail-to-head by specifying how</description>
     <command><![CDATA[
         #if $headers == 0:
@@ -11,11 +11,15 @@
             #if $dataset_names == "No":
                 #for $file in $global_condition.inputs
                     printf "${file.element_identifier}..." &&
-                    #if $file.ext[-2:] == "gz" and $headers != 0:
-                        gzip -dc '$file' | $concat_command | gzip -c >> '$out_file1' &&
-                    #else:
+                    #if $file.ext:
+                        #if $file.ext[-2:] == "gz" and $headers != 0:
+                            gzip -dc '$file' | $concat_command | gzip -c >> '$out_file1' &&
+                        #else:
+                            $concat_command '$file' >> '$out_file1' &&
+                        #end if
+                     #else:
                         $concat_command '$file' >> '$out_file1' &&
-                    #end if
+                     #end if
                     printf "Done\n" &&
                 #end for
                 sleep 1
@@ -399,18 +403,18 @@
             <param name="collection_cat_type" value="two_collections"/>
             <param name="input_1">
                 <collection type="list">
-                    <element name="1_f.fastq" value="1_f.fastq.gz"/>
+                    <element name="1_f.fastq.gz" value="1_f.fastq.gz"/>
                 </collection>
             </param>
             <param name="input_2">
                 <collection type="list">
-                    <element name="1_r.fastq" value="1_r.fastq.gz"/>
+                    <element name="1_r.fastq.gz" value="1_r.fastq.gz"/>
                 </collection>
             </param>
             <param name="dataset_names" value="Yes" />
             <param name="headers" value="4" />
             <output_collection name="list_output" type="list" count="1" >
-                <element name="1_f.fastq_1_r.fastq" file="1_options.fastq.gz" decompress="True"/>
+                <element name="1_f.fastq.gz_1_r.fastq.gz" file="1_options.fastq.gz" decompress="True"/>
             </output_collection>
         </test>
         <test> <!-- Test nested collections concatenation -->
@@ -443,8 +447,8 @@
                 <collection type="list:list">
                     <element name="1">
                         <collection type="list">
-                            <element name="1_f.fastq" value="1_f.fastq.gz" ftype="fastq.gz"/>
-                            <element name="1_r.fastq" value="1_r.fastq.gz" ftype="fastq.gz"/>
+                            <element name="1_f.fastq.gz" value="1_f.fastq.gz" ftype="fastq.gz"/>
+                            <element name="1_r.fastq.gz" value="1_r.fastq.gz" ftype="fastq.gz"/>
                         </collection>
                     </element>
                 </collection>
@@ -460,11 +464,11 @@
 
 .. class:: warningmark
 
-**WARNING:** This tool does not check if the datasets being concatenated are in the same format.
+**WARNINGS:**
 
-**WARNING:** When concatenating 2 collections make sure the first collection is the one with the most items.
-
-**WARNING:** This tool can't handle nested collection deeper than list:list.
+- This tool does not check if the datasets being concatenated are in the same format.
+- When concatenating 2 collections make sure the first collection is the one with the most items.
+- This tool can't handle nested collection deeper than list:list.
 
 -----
 
diff -r 4554fa330d3d -r 55cf9d9defd1 test-data/1_options.fastq.gz
Binary file test-data/1_options.fastq.gz has changed