diff oases_optimiser.xml @ 2:ab37eb09b4ca draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/oases commit d5a2de4b4c556e028fc5ef7ffcc7c2d0cf31c5ec

--- a/oases_optimiser.xml	Sun Mar 07 22:44:05 2021 +0000
+++ b/oases_optimiser.xml	Mon Feb 12 23:55:39 2024 +0000
@@ -1,17 +1,22 @@
-<tool id="oasesoptimiserv" name="Oases_optimiser" version="1.3.0">
+<tool id="oasesoptimiserv" name="Oases_optimiser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Auto optimise de novo RNA-seq Oases/Velvet assembly</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.4.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">23.0</token>
+    </macros>
     <requirements>
         <requirement type="package" version="0.2.09">oases</requirement>
         <requirement type="package" version="1.2.10">velvet</requirement>
-        <requirement type="package" version="3.7.6">python</requirement>
+        <requirement type="package" version="3.12.1">python</requirement>
     </requirements>
     <command><![CDATA[
-	python "$__tool_directory__"/oases_optimiser.py  "$start_hash_length" "$end_hash_length"
-	#for $i in $inputs
-		"${i.input}"
+    python '$__tool_directory__/oases_optimiser.py' '$start_hash_length' '$end_hash_length'
+    #for $i in $inputs
+        '${i.input}'
     #end for
-	"$transcripts"
-	]]></command>
+    '$transcripts'
+    ]]></command>
     <inputs>
         <param label="Start Hash Length" name="start_hash_length" type="select" help="k-mer length in base pairs of the words being hashed. Shorter hash lengths (i.e. less than 31) may cause out-of-memory problems.">
             <option value="11" selected="yes">11</option>
@@ -59,7 +64,7 @@
             </output>
         </test>
     </tests>
-	<help>
+    <help>
 **Oases Optimiser Overview**
 
 Oases_ is a de novo transcriptome assembler specially designed to work with short reads. It is an extension of Velvet developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
@@ -73,21 +78,21 @@
 being run succesively on the data. In the above example, you would find:
 
 transcripts.fa
-	A FASTA file containing the transcripts imputed directly from trivial
-	clusters of contigs (loci with less than two transcripts and Confidence Values = 1)
-	and the highly expressed transcripts imputed by dynamic
-	programming (loci with more than 2 transcripts and Confidence Values less than 1).
+    A FASTA file containing the transcripts imputed directly from trivial
+    clusters of contigs (loci with less than two transcripts and Confidence Values = 1)
+    and the highly expressed transcripts imputed by dynamic
+    programming (loci with more than 2 transcripts and Confidence Values less than 1).
 
 splicing_events.txt
-	A hybrid file which describes the contigs contained in each locus in FASTA
-	format, interlaced with one line descriptions of splicing events using the
-	AStalavista nomenclature*.
+    A hybrid file which describes the contigs contained in each locus in FASTA
+    format, interlaced with one line descriptions of splicing events using the
+    AStalavista nomenclature*.
 
 Read the Oases `documentation`__ for details on using the Oases Assembler.
 
-.. _Oases: http://www.ebi.ac.uk/~zerbino/oases/
+.. _Oases: https://github.com/dzerbino/oases
 
-.. __: http://www.ebi.ac.uk/~zerbino/oases/Manual.txt
+.. __: https://bioweb.pasteur.fr/docs/modules/oases/0.2.08/OasesManual.pdf
 
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