Mercurial > repos > iuc > spades_metaplasmidspades

diff metaplasmidspades.xml @ 7:e5a3b75a271f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
author iuc
date Tue, 23 Aug 2022 08:01:19 +0000
parents 4a01e0d2892c
children 037f9927c4ff
line wrap: on
line diff
--- a/metaplasmidspades.xml	Wed Aug 10 13:16:53 2022 +0000
+++ b/metaplasmidspades.xml	Tue Aug 23 08:01:19 2022 +0000
@@ -22,6 +22,7 @@
 @OMP_THREADS@
 ## run
 spades.py --meta --plasmid
+    $operation_mode
     -o 'output'
     @RESOURCES@
     @INPUT_READS_MAIN@
@@ -42,6 +43,7 @@
     @CORRECTED@
     ]]></command>
     <inputs>
+        <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/>
         <expand macro="input_files_paired" format="fastq, fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/>
         <expand macro="input_additional_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/>
         <section name="arf" title="Additional read files">
@@ -127,17 +129,17 @@
                 </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="71752" 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="71752" 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="423" delta="100"/>
                     </assert_contents>
@@ -187,17 +189,17 @@
             <param name="operation_mode" value="--only-error-correction"/>
             <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="71752" 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="71752" 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="423" delta="100"/>
                     </assert_contents>