Mercurial > repos > jowong > khmer_load_into_counting

changeset 1:f491d18251e9 draft

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planemo upload
author jowong
date Mon, 26 Nov 2018 02:14:27 -0500
parents 69d52f45c2fa
children ab0f91be3a90
files khmer_load_into_counting.xml
diffstat 1 files changed, 8 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/khmer_load_into_counting.xml	Thu Nov 22 09:49:16 2018 -0500
+++ b/khmer_load_into_counting.xml	Mon Nov 26 02:14:27 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="khmer_load_into_counting" name="Load Into Counting" version="0.1.5">
+<tool id="khmer_load_into_counting" name="Load Into Counting" version="1.0.5">
     <description>Creates k-mer countgraph using reads</description>
     <requirements>
         <requirement type="package" version="2.1.2">khmer</requirement>
@@ -7,7 +7,7 @@
         load-into-counting.py
         $advanced.b
         $advanced.small
-        -k $advanced.kmer
+        -k $kmer
         -U $advanced.ukmer
         #if str( $advanced.max_mem ) != "0"
             -M $advanced.max_mem
@@ -15,12 +15,8 @@
         #if str( $advanced.fp_rate ) != "0"
             --fp-rate $advanced.fp_rate
         #end if
-        #if str( $advanced.num_table ) != "0"
-            -N $advanced.num_table
-        #end if
-        #if str( $advanced.table_size ) != "0"
-            -x $advanced.table_size
-        #end if
+        -N $advanced.num_table
+        -x $advanced.table_size
         hash.ct.gz
         #if str( $data_input.data_selector ) == "paired"       
             $data_input.input1.forward $data_input.input1.reverse
@@ -42,14 +38,15 @@
                 <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/>
             </when>
         </conditional>
+        <param name="kmer" type="integer" value="32" label="K-mer" help="K-mer size to use (default: 32)" />
         <section name="advanced" title="Advanced options" expanded="false">
             <param type="boolean" argument="--small" label="Small count" checked="false" truevalue="--small-count" falsevalue="" help="Reduce memory usage by using a smaller counter for individual kmers. (default: False)"/>
             <param type="boolean" argument="-b" label="big count" checked="True" truevalue="-b" falsevalue="--no-bigcount" help="Reduce memory usage by using a smaller counter for individual kmers. (default: True)"/>
             <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" />
-            <param name="kmer" type="integer" value="32" label="K-mer" help="K-mer size to use (default: 32)" />
+            
             <param name="ukmer" type="integer" value="0" label="Unique K-mer" help="approximate number of unique kmers in the input set (default: 0)" />
-            <param name="num_table" type="integer" value="0" label="Number of tables" help="number of tables to use (default: False)" />
-            <param name="table_size" type="integer" value="0" label="Maximum size of table" help="maximum size of tables to use (default: False)" />
+            <param name="num_table" type="integer" value="1" label="Number of tables" help="number of tables to use (default: False)" />
+            <param name="table_size" type="integer" value="1000000000" label="Maximum size of table" help="maximum size of tables to use (default: False)" />
             <param name="max_mem" type="integer" value="0" label="Maximum Memory" help="number of tables to use (default: False)" />
             <param name="fp_rate" type="integer" value="0" label="FP rate override" help="Override the automatic FP rate setting for the current script" />
         </section>