# HG changeset patch
# User kkonganti
# Date 1656368362 14400
# Node ID 3154e7efa1c4a4c4d32185019d2a2daa60d9864a
# Parent  29a590703d3ead003afb22a162483d0643cde66d
"planemo upload"

diff -r 29a590703d3e -r 3154e7efa1c4 cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Mon Jun 27 16:43:05 2022 -0400
+++ b/cfsan_centriflaken.xml	Mon Jun 27 18:19:22 2022 -0400
@@ -7,8 +7,8 @@
     <version_command>nextflow -version</version_command>
     <command detect_errors="exit_code"><![CDATA[
 	mkdir -p cpipes-input &&
-	#for $input in $LIST
-	    ln -sf '$input' './cpipes-input/${input.element_identifier}';
+	#for $input_dataset in $input
+	    ln -sf '$input_dataset' './cpipes-input/${input.element_identifier}';
 	#end for
 	pwd_path=\$(pwd) &&
 	$__tool_directory__/0.2.1/cpipes
@@ -19,13 +19,13 @@
     #end if
 	--input \${pwd_path}/cpipes-input
 	--output \${pwd_path}/cpipes-output
-	#if ($reads_lib.paired_end == "true"):
+	#if ($reads.reads_lib.paired_end == "true"):
 	    --fq_single_end false
-        --fq_suffix '${fq_suffix}'
-	    --fq2_suffix '${fq2_suffix}'
+        --fq_suffix '${reads.reads_lib.fq_suffix}'
+	    --fq2_suffix '${reads.reads_lib.fq2_suffix}'
     #else:
         --fq_single_end true
-        --fq_suffix '${fq_suffix}'
+        --fq_suffix '${reads.fq_suffix}'
 	#end if
 	--fq_filename_delim '${fq_filename_delim}'
 	--fq_filename_delim_idx $fq_filename_delim_idx
@@ -34,7 +34,7 @@
 	-profile $profile
     ]]></command>
     <inputs>
-        <param name="input" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input reads" />
+        <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" />
         <conditional name="reads">
             <param name="type" type="select" label="Sequencing Read Library Type" value="long">
                 <option value="long">Long reads</option>
@@ -79,6 +79,21 @@
             <discover_datasets pattern=".*\.assembly_filtered_contigs.fasta" visible="true" directory="cpipes-output"/>
         </data>
     </outputs>
+    <tests>
+        <!--Test 01: long reads-->
+        <test expect_num_outputs="2">
+            <param name="input" value="FAL11127.fastq.gz" >
+                <collection type="list">
+                    <element name="file1" value="FAL11127.fastq.gz" />
+                    <element name="file2" value="FAL11341.fastq.gz" />
+                    <element name="file3" value="FAL11342.fastq.gz" />
+                </collection>
+            </param>
+            <param name="fq_suffix" value=".fastq.gz"/>
+            <output name="multiqc_report" file="multiqc_report.html" ftype="html" compare="sim_size"/>
+            <output name="assembled_mags" file="FAL11127.assembly_filtered.contigs.fasta" ftype="fasta" compare="sim_size"/>
+        </test>
+    </tests>
     <help><![CDATA[
 
 .. class:: infomark