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changeset 5:2025c7c40396 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit d6846cd9a2228b677e7bc171e67e85e3f3426a00
author iuc
date Mon, 10 Feb 2025 19:16:14 +0000
parents de622e5acd77
children
files macros.xml raven.xml
diffstat 2 files changed, 20 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Mar 21 08:29:07 2022 +0000
+++ b/macros.xml	Mon Feb 10 19:16:14 2025 +0000
@@ -1,6 +1,5 @@
-<?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.8.0</token>
+    <token name="@TOOL_VERSION@">1.8.3</token>
     <token name="@PROFILE@">20.05</token>
     <xml name="requirements">
         <requirements>
@@ -10,6 +9,11 @@
     <xml name="version_command">
         <version_command>raven --version</version_command>
     </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">raven</xref>
+        </xrefs>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1101/2020.08.07.242461</citation>
@@ -25,11 +29,9 @@
     <!--
         input
     -->
-
     <!--
         Help
     -->
-
     <token name="@WID@"><![CDATA[
 *raven* is a de novo genome assembler for long uncorrected reads.
 ]]></token>
--- a/raven.xml	Mon Mar 21 08:29:07 2022 +0000
+++ b/raven.xml	Mon Feb 10 19:16:14 2025 +0000
@@ -1,16 +1,12 @@
-<?xml version="1.0"?>
 <tool id="raven" name="Raven" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>De novo assembly of Oxford Nanopore Technologies data</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
-
     <expand macro="version_command"/>
-
-<!--TODO in future version : enable CUDA support for racon polishing-->
-
+    <!--TODO in future version : enable CUDA support for racon polishing-->
     <command detect_errors="exit_code"><![CDATA[
 #if $input_reads.is_of_type("fasta")
     ln -s '$input_reads' ./input.fa &&
@@ -33,6 +29,10 @@
 --match '$match'
 --mismatch '$mismatch'
 --gap '$gap'
+--kMaxNumOverlaps '$kMaxNumOverlaps'
+--identity $identity
+--min-unitig-size $min_unitig_size
+--use-micromizers $use_micromizers
 $graphical_fragment_assembly
 --disable-checkpoints
 -t \${GALAXY_SLOTS:-4}
@@ -44,17 +44,22 @@
         <param argument="--kmer-len" type="integer" value="15" label="Length of minimizers used to find overlaps"/>
         <param argument="--window-len" type="integer" value="5" label="Length of sliding window from which minimizers are sampled"/>
         <param argument="--frequency" type="float" value="0.001" label="Threshold for ignoring most frequent minimizers"/>
+        <param argument="--identity" type="float" value="0" label="Threshold for overlap between two reads in order to construct an edge between them" help="If set to zero, this functionality is disabled"/>
+        <param argument="--kMaxNumOverlaps" type="integer" value="32" label="Maximum number of overlaps that will be taken during FindOverlapsAndCreatePiles stage"/>
+        <param argument="--min-unitig-size" type="integer" value="9999" label="Minimal unitig size"/>
+
         <param argument="--polishing-rounds" type="integer" value="2" min="0" label="Number of times racon polishing is invoked"/>
         <param argument="--match" type="integer" value="3"/>
         <param argument="--mismatch" type="integer" value="-5"/>
         <param argument="--gap" type="integer" value="-4" max="-1"/>
         <param argument="--graphical-fragment-assembly" type="boolean" truevalue="--graphical-fragment-assembly out.gfa" falsevalue="" label="output graphical fragment assembly file?" checked="true"/>
+        <param argument="--use-micromizers" type="boolean" truevalue="--use-micromizers" falsevalue="" label="Use micromizers instead of mimizers in graph construction" help="Performance will increase slightly and memory consumption will decrease but results could be slightly worse"/>
     </inputs>
     <outputs>
         <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)" from_work_dir="out.gfa">
             <filter>graphical_fragment_assembly</filter>
         </data>
-        <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)" />
+        <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)"/>
     </outputs>
     <tests>
         <test expect_num_outputs="2">
@@ -62,13 +67,13 @@
             <output name="out_gfa">
                 <assert_contents>
                     <has_n_lines n="2"/>
-                    <has_text_matching expression="^S\tUtg52\t[ATCG]{30000,40000}\tLN:i:36[0-9]{3}\tRC:i:22\nS\tCtg54\t[ATCG]{9000,10000}\tLN:i:9361\tRC:i:4"/>
+                    <has_text_matching expression="^S\tUtg52\t[ATCG]{30000,40000}\tLN:i:36[0-9]{3}\tRC:i:22\tdp:f:8\nS\tCtg54\t[ATCG]{9000,10000}\tLN:i:9361\tRC:i:4"/>
                 </assert_contents>
             </output>
             <output name="out_fasta">
                 <assert_contents>
                     <has_n_lines n="2"/>
-                    <has_text_matching expression="^>Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/>
+                    <has_text_matching expression="^&gt;Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/>
                 </assert_contents>
             </output>
         </test>