Mercurial > repos > lparsons > cutadapt

diff cutadapt.xml @ 29:48f587c13075 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
author iuc
date Thu, 10 Feb 2022 12:13:05 +0000
parents c053d4cad713
children c5e2e5902201
line wrap: on
line diff
--- a/cutadapt.xml	Sat Nov 27 10:09:14 2021 +0000
+++ b/cutadapt.xml	Thu Feb 10 12:13:05 2022 +0000
@@ -93,13 +93,8 @@
 #else:
     @read1_options@
     @read2_options@
-    #if $library.type == "paired"
-        --output='$out1'
-        --paired-output='$out2'
-    #else
-        --output='$out_pairs.forward'
-        --paired-output='$out_pairs.reverse'
-    #end if
+    --output='$out1'
+    --paired-output='$out2'
 #end if
 
 --error-rate=$adapter_options.error_rate
@@ -337,6 +332,8 @@
 
         <collection name="out_pairs" type="paired" format_source="input_1" label="${tool.name} on ${on_string}: Reads">
             <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter>
+            <data name="forward" from_work_dir="out1.fq*" />
+            <data name="reverse" from_work_dir="out2.fq*" />
         </collection>
         
         <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report">
@@ -478,9 +475,17 @@
                     </conditional>
                 </repeat>
             </section>
-            <output_collection name="out_pairs" type="paired">
-                <element name="forward" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz" />
-                <element name="reverse" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz" />
+            <output_collection name="out_pairs" type="paired" count="2">
+                <element name="forward" decompress="true" file="cutadapt_out1.fq.gz" ftype="fastq.gz">
+                    <assert_contents>
+                        <has_size value="12000" delta="2000" />
+                    </assert_contents>
+                </element>
+                <element name="reverse" decompress="true" file="cutadapt_out2.fq.gz" ftype="fastq.gz">
+                    <assert_contents>
+                        <has_size value="12000" delta="2000" />
+                    </assert_contents>
+                </element>
             </output_collection>
         </test>
         <!-- Ensure built-in adapters work -->