diff rnaviralspades.xml @ 7:d5fb354f745d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2

--- 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>