# HG changeset patch
# User iuc
# Date 1660137442 0
# Node ID ff41a00a674587d6fa7ac503a2eeb2c12e705fc5
# Parent  fee85957cebe4cdc8cea9724856f4d47c92f8f6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3

diff -r fee85957cebe -r ff41a00a6745 coronaspades.xml
--- a/coronaspades.xml	Wed Jul 13 07:44:04 2022 +0000
+++ b/coronaspades.xml	Wed Aug 10 13:17:22 2022 +0000
@@ -19,6 +19,7 @@
 @PREPROCESS_SANGER_FILES@
 
 
+@OMP_THREADS@
 ## run
 coronaspades.py
     -o 'output'
@@ -162,7 +163,7 @@
 
 **References**
 
-More information can be found on `github <https://github.com/ablab/spades>`_  and on the `project website <https://cab.spbu.ru/software/coronaspades/>`_.
+More information can be found on `github <https://github.com/ablab/spades>`_.
     ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1093/bioinformatics/btab597</citation>
diff -r fee85957cebe -r ff41a00a6745 macros.xml
--- a/macros.xml	Wed Jul 13 07:44:04 2022 +0000
+++ b/macros.xml	Wed Aug 10 13:17:22 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.15.4</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
@@ -43,6 +43,9 @@
         </param>
     </xml>
     
+<token name="@OMP_THREADS@"><![CDATA[
+export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
+]]></token>
 
 <!-- PREPARE INPUT FILES-->
 
@@ -738,7 +741,7 @@
 SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
     </token>
     <token name="@IONTORRENT@"><![CDATA[
-The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our `recommendation for long reads <https://cab.spbu.ru/files/release3.12.0/manual.html#sec3.4>`_ (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o <previous_output_dir>. Do not forget to copy contigs and scaffolds from the previous run. We're planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions.
+The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our `recommendation for long reads <https://github.com/ablab/spades#sec3.4>`_ (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o <previous_output_dir>. Do not forget to copy contigs and scaffolds from the previous run. We're planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions.
 
 You may need no error correction for Hi-Q enzyme at all. However, we suggest trying to assemble your data with and without error correction and select the best variant.