# HG changeset patch
# User iuc
# Date 1661241605 0
# Node ID 1708851f8804e95701dc3a68f5e0fc9c6f1c3592
# Parent  75405f5e2cc5209a6361e642c0eaf2d05d4db336
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2

diff -r 75405f5e2cc5 -r 1708851f8804 macros.xml
--- a/macros.xml	Wed Aug 10 13:15:28 2022 +0000
+++ b/macros.xml	Tue Aug 23 08:00:05 2022 +0000
@@ -601,34 +601,34 @@
     <xml name="out_ag">
         <data name="out_ag" format="fastg" from_work_dir="output/assembly_graph.fastg" label="${tool.name} on ${on_string}: Assembly graph">
             <filter>'ag' in optional_output</filter>
-            <filter> operation_mode != '--only-error-correction'</filter>
+            <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
         </data>
     </xml>
     <xml name="out_ags">
         <data name="out_ags" format="txt" from_work_dir="output/assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: Assembly graph with scaffolds">
             <filter>'ags' in optional_output</filter>
-            <filter> operation_mode != '--only-error-correction'</filter>
+            <filter>'operation_mode' not in vars() or  operation_mode != '--only-error-correction'</filter>
         </data>
     </xml>
     <xml name="out_cn">
         <data name="out_cn" format="fasta" from_work_dir="output/contigs.fasta" label="${tool.name} on ${on_string}: Contigs">
             <filter>'cn' in optional_output</filter>
-            <filter> operation_mode != '--only-error-correction'</filter>
+            <filter>'operation_mode' not in vars() or  operation_mode != '--only-error-correction'</filter>
         </data>
     </xml>
     <xml name="out_cp">
         <data name="out_cp" format="txt" from_work_dir="output/contigs.paths" label="${tool.name} on ${on_string}: Contigs paths">
             <filter>'cp' in optional_output</filter>
-            <filter> operation_mode != '--only-error-correction'</filter>
+            <filter>'operation_mode' not in vars() or  operation_mode != '--only-error-correction'</filter>
         </data>
     </xml>
     <xml name="out_cr">
         <!-- some mode combinations create fastq, some fasta -->
         <collection name="out_cr" type="list" label="${tool.name} on ${on_string}: Corrected reads">
             <filter>'cr' in optional_output</filter>
-            <filter> operation_mode != '--only-assembler'</filter>
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastq\.gz" format="fastq" directory="output/corrected"/>
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta\.gz" format="fasta" directory="output/corrected"/>
+            <filter>'operation_mode' not in vars() or operation_mode != '--only-assembler'</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.cor\.fastq\.gz" format="fastq" directory="output/corrected"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.cor\.fasta\.gz" format="fasta" directory="output/corrected"/>
         </collection>
     </xml>
     <xml name="out_cs">
@@ -637,7 +637,7 @@
                 <action name="column_names" type="metadata" default="name,length,coverage"/>
             </actions>
             <filter>'cs' in optional_output</filter>
-            <filter> operation_mode != '--only-error-correction'</filter>
+            <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
         </data>
     </xml>
     <xml name="out_l">
@@ -648,13 +648,13 @@
     <xml name="out_sc">
         <data name="out_sc" format="fasta" from_work_dir="output/scaffolds.fasta" label="${tool.name} on ${on_string}: Scaffolds">
             <filter>'sc' in optional_output</filter>
-            <filter> operation_mode != '--only-error-correction'</filter>
+            <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
         </data>
     </xml>
     <xml name="out_sp">
         <data name="out_sp" format="txt" from_work_dir="output/scaffolds.paths" label="${tool.name} on ${on_string}: Scaffolds paths">
             <filter>'sp' in optional_output</filter>
-            <filter> operation_mode != '--only-error-correction'</filter>
+            <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
         </data>
     </xml>
     <xml name="out_ss">
@@ -663,7 +663,7 @@
                 <action name="column_names" type="metadata" default="name,length,coverage"/>
             </actions>
             <filter>'ss' in optional_output</filter>
-            <filter> operation_mode != '--only-error-correction'</filter>
+            <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
         </data>
     </xml>
     <xml name="out_rs">
diff -r 75405f5e2cc5 -r 1708851f8804 plasmidspades.xml
--- a/plasmidspades.xml	Wed Aug 10 13:15:28 2022 +0000
+++ b/plasmidspades.xml	Tue Aug 23 08:00:05 2022 +0000
@@ -162,17 +162,17 @@
                 </assert_contents>
             </output>
             <output_collection name="out_cr" type="list" count="3">
-                <element name="pl1.fq.gz.fastq.00.0_0.cor">
+                <element name="pl1.fq.gz.fastq.00.0_0">
                     <assert_contents>
                         <has_size value="72173" delta="1000"/>
                     </assert_contents>
                 </element>
-                <element name="pl2.fq.gz.fastq.00.0_0.cor">
+                <element name="pl2.fq.gz.fastq.00.0_0">
                     <assert_contents>
                         <has_size value="72173" delta="1000"/>
                     </assert_contents>
                 </element>
-                <element name="pl_unpaired.00.0_0.cor">
+                <element name="pl_unpaired.00.0_0">
                     <assert_contents>
                         <has_size value="392" delta="100"/>
                     </assert_contents>
@@ -251,17 +251,17 @@
             </conditional>
             <param name="optional_output" value="cr,l"/>
             <output_collection name="out_cr" type="list" count="3">
-                <element name="pl1.fq.gz.fastq.00.0_0.cor">
+                <element name="pl1.fq.gz.fastq.00.0_0">
                     <assert_contents>
                         <has_size value="72173" delta="1000"/>
                     </assert_contents>
                 </element>
-                <element name="pl2.fq.gz.fastq.00.0_0.cor">
+                <element name="pl2.fq.gz.fastq.00.0_0">
                     <assert_contents>
                         <has_size value="72173" delta="1000"/>
                     </assert_contents>
                 </element>
-                <element name="pl_unpaired.00.0_0.cor">
+                <element name="pl_unpaired.00.0_0">
                     <assert_contents>
                         <has_size value="392" delta="100"/>
                     </assert_contents>
@@ -283,17 +283,17 @@
             </conditional>
             <param name="optional_output" value="cr,l"/>
             <output_collection name="out_cr" type="list" count="3">
-                <element name="pl1.fq.gz.fastq.00.0_0.cor">
+                <element name="pl1.fq.gz.fastq.00.0_0">
                     <assert_contents>
                         <has_size value="72173" delta="1000"/>
                     </assert_contents>
                 </element>
-                <element name="pl2.fq.gz.fastq.00.0_0.cor">
+                <element name="pl2.fq.gz.fastq.00.0_0">
                     <assert_contents>
                         <has_size value="72173" delta="1000"/>
                     </assert_contents>
                 </element>
-                <element name="pl_unpaired.00.0_0.cor">
+                <element name="pl_unpaired.00.0_0">
                     <assert_contents>
                         <has_size value="392" delta="100"/>
                     </assert_contents>
@@ -327,17 +327,17 @@
             <param name="mode_sel" value="--careful"/>
             <param name="optional_output" value="cr,l"/>
             <output_collection name="out_cr" type="list" count="3">
-                <element name="pl1.fq.gz.fastq.00.0_0.cor">
+                <element name="pl1.fq.gz.fastq.00.0_0">
                     <assert_contents>
                         <has_size value="72173" delta="1000"/>
                     </assert_contents>
                 </element>
-                <element name="pl2.fq.gz.fastq.00.0_0.cor">
+                <element name="pl2.fq.gz.fastq.00.0_0">
                     <assert_contents>
                         <has_size value="72173" delta="1000"/>
                     </assert_contents>
                 </element>
-                <element name="pl_unpaired.00.0_0.cor">
+                <element name="pl_unpaired.00.0_0">
                     <assert_contents>
                         <has_size value="392" delta="100"/>
                     </assert_contents>