# HG changeset patch
# User fubar
# Date 1708747887 0
# Node ID 27df186d544659da1c65b49793b88eabe1ccd972
# Parent  10e4181a644378b6f004583245cf96aefdf3aa4c
planemo upload

diff -r 10e4181a6443 -r 27df186d5446 mashmap.xml
--- a/mashmap.xml	Fri Feb 23 09:59:25 2024 +0000
+++ b/mashmap.xml	Sat Feb 24 04:11:27 2024 +0000
@@ -1,6 +1,6 @@
 <tool name="mashmap" id="mashmap" version="3.1.3" profile="22.05">
   <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
-  <!--Created by toolfactory@galaxy.org at 23/02/2024 20:50:55 using the Galaxy Tool Factory.-->
+  <!--Created by toolfactory@galaxy.org at 23/02/2024 21:34:16 using the Galaxy Tool Factory.-->
   <description>Fast local alignment boundaries</description>
   <requirements>
     <requirement version="3.1.3" type="package">mashmap</requirement>
@@ -11,9 +11,9 @@
     <configfile name="runme"><![CDATA[#if len($reflist) > 1:
 #for i, mash in enumerate($reflist):
    #if i == 0:
-       echo $mash > 'reflist' &&
+       echo '$mash' > 'reflist' &&
    #else:
-       echo $mash >> 'reflist' &&
+       echo '$mash' >> 'reflist' &&
    #end if
 #end for
 #end if
@@ -22,11 +22,11 @@
 -J '$sketchSize' \
 #end if
 #if len($reflist) == 1:
- -r $reflist -q '$query' && 
+ -r '$reflist' -q '$query' && 
 #else
 --rl 'reflist' -q '$query' && 
 #end if
-cp 'mashmap.out'  $mashout]]></configfile>
+cp 'mashmap.out'  '$mashout']]></configfile>
   </configfiles>
   <inputs>
     <param name="query" type="data" optional="false" label="Query sequences (as fasta) to mash against the references supplied below" help="" format="fasta" multiple="false"/>
@@ -70,7 +70,8 @@
  
  mashmap -r reference.fna -q query.fa
  
- 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.
+ 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.
  
  Map set of query seqences against a list of reference genomes: