# HG changeset patch
# User iuc
# Date 1661241556 0
# Node ID d5fb354f745de8fa63c2d0ce5a6f4132cbdcb5b5
# Parent  48cf45a534566b31d2b696e1dcbe1e18d7a19a51
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2

diff -r 48cf45a53456 -r d5fb354f745d macros.xml
--- a/macros.xml	Wed Aug 10 13:14:28 2022 +0000
+++ b/macros.xml	Tue Aug 23 07:59:16 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 48cf45a53456 -r d5fb354f745d rnaviralspades.xml
--- a/rnaviralspades.xml	Wed Aug 10 13:14:28 2022 +0000
+++ b/rnaviralspades.xml	Tue Aug 23 07:59:16 2022 +0000
@@ -21,6 +21,7 @@
 @OMP_THREADS@
 ## run
 spades.py --rnaviral
+    $operation_mode
     -o 'output'    
     @RESOURCES@
     @INPUT_READS_MAIN@
@@ -41,6 +42,7 @@
     @CORRECTED@
     ]]></command>
     <inputs>
+        <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/>
         <expand macro="input_files_all" format="fastq,fasta,fastq.gz,fastqsanger.gz,fasta.gz" label="FASTQ RNA-seq file(s)"/>
         <expand macro="input_additional_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTQ RNA-seq file(s)"/>
         <section name="arf" title="Additional read files">
@@ -144,13 +146,13 @@
                     <has_n_lines n="0"/>
                 </assert_contents>
             </output>
-            <output_collection name="out_cr" type="list" count="4">
-                <element name="ecoli_1K_1.fastq.gz.fastq0_0.cor">
+            <output_collection name="out_cr" type="list" count="2">
+                <element name="ecoli_1K_1.fastq.gz.fastq0_0">
                     <assert_contents>
                         <has_size value="34468" delta="2000"/>
                     </assert_contents>
                 </element>
-                <element name="ecoli_1K_2.fastq.gz.fastq0_0.cor">
+                <element name="ecoli_1K_2.fastq.gz.fastq0_0">
                     <assert_contents>
                         <has_size value="34468" delta="2000"/>
                     </assert_contents>