# HG changeset patch
# User iuc
# Date 1618768108 0
# Node ID dfefaf2bab9535d6f8a3c32959258edbda628936
# Parent  6de3e77073ad62d68f6201509231c676a915310a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"

diff -r 6de3e77073ad -r dfefaf2bab95 disco.xml
--- a/disco.xml	Wed May 02 05:47:09 2018 -0400
+++ b/disco.xml	Sun Apr 18 17:48:28 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="disco" name="DISCO" version="@WRAPPER_VERSION@.0">
+<tool id="disco" name="DISCO" version="@WRAPPER_VERSION@.1" profile="20.01">
     <description>to assemble metagenomics data using an overlap-layout-consensus (OLC) approach</description>
     <macros>
         <token name="@WRAPPER_VERSION@">1.2</token>
@@ -20,21 +20,55 @@
     <requirements>
         <requirement type="package" version="@WRAPPER_VERSION@">disco</requirement>
     </requirements>
-    <version_command>runDisco.sh --version</version_command>
+    <version_command>echo @WRAPPER_VERSION@</version_command>
     <command detect_errors="exit_code"><![CDATA[
+#if $input_cond.library_type == "single"
+    #for i, e in enumerate($input_cond.inS)
+        cp '$e'
+        #if $e.ext.endswith(".gz")
+            input_${i}.fastq.gz &&
+        #else
+            input_${i}.fastq &&
+        #end if
+    #end for
+#else
+    #if $input_cond.paired_input.type == "separated"
+        #if $input_cond.paired_input.in1.ext.endswith(".gz")
+           cp '$input_cond.paired_input.in1' forward.fastq.gz &&
+           cp '$input_cond.paired_input.in2' reverse.fastq.gz &&
+        #else
+           cp '$input_cond.paired_input.in1' forward.fastq &&
+           cp '$input_cond.paired_input.in2' reverse.fastq &&
+        #end if
+    #else
+        #for i, e in enumerate($input_cond.paired_input.inP)
+            cp '$e'
+            #if $e.ext.endswith(".gz")
+                input_${i}.fastq.gz &&
+            #else
+                input_${i}.fastq &&
+            #end if
+        #end for
+    #end if
+#end if
 runDisco.sh
     -n \${GALAXY_SLOTS:-4}
     -m \${DISCO_MAX_MEMORY:-4}
     -d .
     -o disco
-    #if $input.library_type == "single"
-        -inS '$input.inS'
+    #if $input_cond.library_type == "single"
+        -inS \$(find . -name "*fastq*" -print | tr '\n' ',' | sed 's/,$//')
     #else
-        #if $input.paired_input.type == "separated"
-            -in1 '$input.paired_input.in1'
-            -in2 '$input.paired_input.in2'
+        #if $input_cond.paired_input.type == "separated"
+            #if $input_cond.paired_input.in1.ext.endswith(".gz") 
+                -in1 forward.fastq.gz
+                -in2 reverse.fastq.gz
+            #else
+                -in1 forward.fastq
+                -in2 reverse.fastq
+            #end if
         #else
-            -inP '$input.paired_input.inP'
+            -inP \$(find . -name "*fastq*" -print | tr '\n' ',' | sed 's/,$//')
         #end if
     #end if
     $obg
@@ -109,13 +143,13 @@
         ]]></configfile>
     </configfiles>
     <inputs>
-        <conditional name="input">
+        <conditional name="input_cond">
             <param name="library_type" type="select" label="Type of library?">
                 <option value="single">Single-end reads</option>
                 <option value="paired">Paired-end reads</option>
             </param>
             <when value="single">
-                <param argument="-inS" type="data" format="fastq,fasta" multiple="true" label="Single-read files"/>
+                <param argument="-inS" type="data" format="fastq,fastq.gz,fasta" multiple="true" label="Single-read files"/>
             </when>
             <when value="paired">
                 <conditional name="paired_input">
@@ -124,11 +158,11 @@
                         <option value="interleaved">Interleaved paired-read files</option>
                     </param>
                     <when value="separated">
-                        <param argument="-in1" type="data" format="fastq,fasta" label="Forward read file" />
-                        <param argument="-in2" type="data" format="fastq,fasta" label="Reverse read file" />
+                        <param argument="-in1" type="data" format="fastq,fastq.gz,fasta" label="Forward read file" />
+                        <param argument="-in2" type="data" format="fastq,fastq.gz,fasta" label="Reverse read file" />
                     </when>
                     <when value="interleaved">
-                        <param argument="-inP" type="data" format="fastq,fasta" multiple="true" label="Interleaved paired-read files" />
+                        <param argument="-inP" type="data" format="fastq,fastq.gz,fasta" multiple="true" label="Interleaved paired-read files" />
                     </when>
                 </conditional>
             </when>
@@ -172,7 +206,7 @@
     </outputs>
     <tests>
         <test>
-            <conditional name="input">
+            <conditional name="input_cond">
                 <param name="library_type" value="paired"/>
                 <conditional name="paired_input">
                     <param name="type" value="separated"/>
@@ -265,7 +299,7 @@
             </output_collection>
         </test>
         <test>
-            <conditional name="input">
+            <conditional name="input_cond">
                 <param name="library_type" value="paired"/>
                 <conditional name="paired_input">
                     <param name="type" value="interleaved"/>
@@ -333,9 +367,9 @@
             <output name="scaffolds" value="test2_scaffolds.fasta" compare="sim_size" delta="5"/>
         </test>
         <test>
-            <conditional name="input">
+            <conditional name="input_cond">
                 <param name="library_type" value="single"/>
-                <param name="inS" value="ecoli_1K_1.fq"/>
+                <param name="inS" value="ecoli_1K_1.fq.gz" ftype="fastq.gz"/>
             </conditional>
             <param name="obg" value=""/>
             <param name="osg" value=""/>
@@ -393,7 +427,8 @@
     <help><![CDATA[
 DISCO is a multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler. Disco was developed as a scalable assembler to assemble large metagenomes from billions of Illumina sequencing reads of complex microbial communities. Disco was parallelized for computer clusters in a hybrid architecture that integrated shared-memory multi-threading, point-to-point message passing, and remote direct memory access. The assembly and scaffolding were performed using an iterative overlap graph approach.
 
-The detailed user manual of the assembler and how to use it to acheive best results is provided here: http://disco.omicsbio.org/user-manual. This is a quick start guide generally for developers and testers. Users with limited experience with genome assembly are advised to use the user manual.
+The detailed user manual of the assembler and how to use it to acheive best results is provided here:
+ http://disco.omicsbio.org/user-manual. This is a quick start guide generally for developers and testers. Users with limited experience with genome assembly are advised to use the user manual.
     ]]></help>
     <citations>
     </citations>
diff -r 6de3e77073ad -r dfefaf2bab95 test-data/ecoli_1K_1.fq.gz
Binary file test-data/ecoli_1K_1.fq.gz has changed
diff -r 6de3e77073ad -r dfefaf2bab95 test-data/ecoli_1K_2.fq.gz
Binary file test-data/ecoli_1K_2.fq.gz has changed