Mercurial > repos > dfornika > mash_sketch

changeset 1:ca04184270ba draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit b1e065ba7e15f9f10b969db1d561b0e8fe6d4572-dirty"
author dfornika
date Fri, 14 Feb 2020 19:31:10 +0000
parents 70e20e8ccdaf
children 4cabc0861a9b
files mash_sketch.xml
diffstat 1 files changed, 9 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/mash_sketch.xml	Fri Feb 14 18:56:53 2020 +0000
+++ b/mash_sketch.xml	Fri Feb 14 19:31:10 2020 +0000
@@ -13,8 +13,10 @@
         mash sketch
             -s '${sketch_size}'
             -k '${kmer_size}'
-            -m '${minimum_kmer_copies}'
             #if str ( $reads_assembly.reads_assembly_selector ) == "reads"
+              -b '${bloom_filter_size}'
+              -m '${minimum_kmer_copies}'
+              -c '${target_coverage}'
               -r
               #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired"
                 '$reads_input.reads_1' '$reads_input.reads_2'
@@ -55,15 +57,19 @@
                         <param name="reads" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
                     </when>
                 </conditional>
+                <param type="string" name="bloom_filter_size" argument="-b" label="Bloom filter size" help="raw bytes or with K/M/G/T"/>
+                <param type="integer" name="minimum_kmer_copies" argument="-m" value="1" min="1" max="1000" label="Minimum copies of each k-mer required to pass noise filter"/>
+                <param type="float" name="target_coverage" argument="-c" value="1." min="0." max="100." label="Target coverage"/>
+                
             </when>
             <when value="assembly">
                 <param name="assembly" type="data" format="fasta,fasta.gz" label="Assembly"/>
-                <param type="boolean" name="individual_sequences" truevalue="-i" falsevalue="" label="Sketch individual Sequences"/> 
+                <param type="boolean" name="individual_sequences" truevalue="-i" falsevalue="" label="Sketch individual Sequences"/>
             </when>
         </conditional>
         <param type="integer" name="sketch_size" argument="-s" value="1000" min="10" max="1000000" />
         <param type="integer" name="kmer_size" argument="-k" value="21" min="1" max="32"/>
-        <param type="integer" name="minimum_kmer_copies" argument="-m" value="1" min="1" max="1000"/>
+        
     </inputs>
     <outputs>
         <data name="sketch" format="msh" from_work_dir="sketch.msh"/>