Mercurial > repos > iuc > spades_metaviralspades

changeset 8:5b26685e5d3b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 066e075c1599b29e92708194db2b2ccc30b7677c
author iuc
date Mon, 12 Feb 2024 21:46:08 +0000
parents 328aa71f0f3c
children 7922870efcca
files macros.xml metaviralspades.xml
diffstat 2 files changed, 7 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Aug 23 08:00:30 2022 +0000
+++ b/macros.xml	Mon Feb 12 21:46:08 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">3.15.4</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">3.15.5</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
@@ -504,10 +504,6 @@
             </param>
             <when value="true">
                 <expand macro="input_files_paired" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)" help="@HELP@"/>
-                <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the sample sample, it means that they belong to the same library.">
-                    <option value="true" selected="true">True</option>
-                    <option value="false">False</option>
-                </param>
             </when>
             <when value="false"/>
         </conditional>
--- a/metaviralspades.xml	Tue Aug 23 08:00:30 2022 +0000
+++ b/metaviralspades.xml	Mon Feb 12 21:46:08 2024 +0000
@@ -3,6 +3,9 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">metaviralspades</xref>
+    </xrefs>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>
@@ -22,6 +25,7 @@
 @OMP_THREADS@
 ## run
 spades.py --metaviral
+    $operation_mode
     -o 'output'
     @RESOURCES@
     @INPUT_READS_MAIN@
@@ -52,6 +56,7 @@
         </section>
         <expand macro="kmer"/>
         <expand macro="phred"/>
+        <expand macro="operation_mode"/>
         <expand macro="pipeline_options">
             <option value="--careful">Careful: ties to reduce the number of mismatches and short indels. Only recommended for small genomes (--careful)</option>
             <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>