diff mashmap.xml @ 3:aa2234f3b23a draft

planemo upload

--- a/mashmap.xml	Thu Feb 22 10:49:45 2024 +0000
+++ b/mashmap.xml	Fri Feb 23 09:13:49 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 [e-mail] at 22/02/2024 21:43:25 using the Galaxy Tool Factory.-->
+  <!--Created by [e-mail] at 23/02/2024 20:10:51 using the Galaxy Tool Factory.-->
   <description>Fast local alignment boundaries</description>
   <requirements>
     <requirement version="3.1.3" type="package">mashmap</requirement>
@@ -12,23 +12,22 @@
 #if int($sketchSize) > 0:
 -J '$sketchSize' \
 #end if
-#if '$dense':
+#if '$dense' == 'set':
 --dense \
 #end if
 #if len($reflist) == 1:
- -r '$reflist' -q '$query' 
+ -r $reflist -q '$query' 
 #else
-rm -rf 'reflist'
 #for i, mash in enumerate($reflist):
    #if i == 0:
-       echo '$mash' > 'reflist'
+       echo $mash > 'reflist'
    #else:
-       echo '$mash' >> 'reflist'
+       echo $mash >> 'reflist'
    #end if
 #end for
 --rl  'reflist' -q '$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"/>
@@ -36,7 +35,10 @@
     <param name="perc_identity" type="float" value="85.0" label="Identity threshold" help="By default, it is set to 85, implying mappings with 85 or more identity should be reported. For example, it can be set to 80to account for more noisy long-read datasets or 95 for mapping human genome assembly to human reference."/>
     <param name="seqLength" type="integer" value="5000" label="Minimum segment length" help="Default is 5,000 bp. Sequences below this length are ignored. Mashmap provides guarantees on reporting local alignments of length twice this value."/>
     <param name="sketchSize" type="integer" value="0" label="Sketch size - leave 0 for automatic setting based" help="This parameter sets the seed density of the winnowing scheme, gauranteeing that the minhash will be calculated from a sample of sketchSize k-mers for each segment. It is set automatically based on --pi but can be manually set as well."/>
-    <param name="dense" type="boolean" value="false" label="Dense sketching" help="This flag will increase the seed density substantially, resulting in a density of roughly 0.02 * (1 + (1 - pi) / .05) where pi is the perc_identity threshold. This leads to longer runtimes and higher RAM usage, but significantly more accurate estimates of ANI." checked="false" truevalue="--dense" falsevalue=""/>
+    <param name="dense" type="select" label="Dense sketching" help="This flag will increase the seed density substantially, resulting in a density of roughly 0.02 * (1 + (1 - pi) / .05) where pi is the perc_identity threshold. This leads to longer runtimes and higher RAM usage, but significantly more accurate estimates of ANI." display="radio">
+      <option value="notset">Do not set this flag</option>
+      <option value="set">Set this flag</option>
+    </param>
     <param name="filtermode" type="select" label="Filter mode" help="Mashmap implements a plane-sweep based algorithm to perform the alignment filtering. Similar to delta-filter in nucmer, different filtering options are provided that are suitable for long read or assembly mapping. Option -f map is suitable for reporting the best mappings for long reads, whereas -f one-to-one is suitable for reporting orthologous mappings among all computed assembly to genome mappings.">
       <option value="map">map - best mapping for long reads</option>
       <option value="one-to-one">one-to-one - best for mapping orthologous reads</option>
@@ -54,7 +56,7 @@
       <param name="perc_identity" value="85.0"/>
       <param name="seqLength" value="5000"/>
       <param name="sketchSize" value="0"/>
-      <param name="dense" value="false"/>
+      <param name="dense" value="notset"/>
       <param name="filtermode" value="map"/>
     </test>
   </tests>