# HG changeset patch
# User fubar
# Date 1708749156 0
# Node ID 53f601fb8664dc445115ca450e5605e17c6ccbc3
# Parent  27df186d544659da1c65b49793b88eabe1ccd972
planemo upload

diff -r 27df186d5446 -r 53f601fb8664 mashmap.xml
--- a/mashmap.xml	Sat Feb 24 04:11:27 2024 +0000
+++ b/mashmap.xml	Sat Feb 24 04:32:36 2024 +0000
@@ -1,11 +1,12 @@
-<tool name="mashmap" id="mashmap" version="3.1.3" profile="22.05">
+<tool name="mashmap" id="mashmap" version="1.19.2" profile="22.05">
   <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
-  <!--Created by toolfactory@galaxy.org at 23/02/2024 21:34:16 using the Galaxy Tool Factory.-->
+  <!--Created by toolfactory@galaxy.org at 24/02/2024 15:30:44 using the Galaxy Tool Factory.-->
   <description>Fast local alignment boundaries</description>
   <requirements>
     <requirement version="3.1.3" type="package">mashmap</requirement>
+    <requirement version="1.19.2" type="package">samtools</requirement>
   </requirements>
-  <version_command><![CDATA[echo "3.1.3"]]></version_command>
+  <version_command><![CDATA[echo "1.19.2"]]></version_command>
   <command><![CDATA[bash '$runme']]></command>
   <configfiles>
     <configfile name="runme"><![CDATA[#if len($reflist) > 1:
@@ -17,6 +18,7 @@
    #end if
 #end for
 #end if
+samtools faidx '$query' &&
 mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \
 #if int($sketchSize) > 0:
 -J '$sketchSize' \
@@ -70,8 +72,7 @@
  
  mashmap -r reference.fna -q query.fa
  
- The output is a paf format file (https://github.com/lh3/miniasm/blob/master/PAF.md).
- Thi is space-delimited with each line consisting of query name, length, 0-based start, end, strand, target name, length, start, end and mapping nucleotide identity.
+ The output is space-delimited with each line consisting of query name, length, 0-based start, end, strand, target name, length, start, end and mapping nucleotide identity.
  
  Map set of query seqences against a list of reference genomes: