Mercurial > repos > jowong > khmer_load_into_counting

comparison khmer_load_into_counting.xml @ 1:54ae5353e3e9 draft

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planemo upload
author jowong
date Tue, 13 Nov 2018 13:15:20 -0500
parents 57363aa37022
children 57daf7463a42
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0:57363aa37022 1:54ae5353e3e9
1 <tool id="khmer_load_into_counting" name="Load Into Counting" version="0.1.0"> 1 <tool id="khmer_load_into_counting" name="Load Into Counting" version="0.1.1">
2 <description>Creates k-mer countgraph using reads</description> 2 <description>Creates k-mer countgraph using reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.1.2">khmer</requirement> 4 <requirement type="package" version="2.1.2">khmer</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 load_into_counting.py 7 load_into_counting.py
8 $advanced.b 8 $advanced.b
9 $advanced.small-count 9 $advanced.small
10 -k $advanced.kmer 10 -k $advanced.kmer
11 -U $advanced.ukmer 11 -U $advanced.ukmer
12 #if str( $advanced.max_mem ) != "0" 12 #if str( $advanced.max_mem ) != "0"
13 -M $advanced.max_mem 13 -M $advanced.max_mem
14 #end if 14 #end if
41 <when value="single"> 41 <when value="single">
42 <param name="input2" format="data" type="data_collection" label="input" help="Specify dataset with single reads"/> 42 <param name="input2" format="data" type="data_collection" label="input" help="Specify dataset with single reads"/>
43 </when> 43 </when>
44 </conditional> 44 </conditional>
45 <section name="advanced" title="Advanced options" expanded="false"> 45 <section name="advanced" title="Advanced options" expanded="false">
46 <param type="boolean" argument="--small-count" label="Small count" checked="false" truevalue="--small-count" falsevalue="" help="Reduce memory usage by using a smaller counter for individual kmers. (default: False)"/> 46 <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)"/>
47 <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)"/> 47 <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)"/>
48 <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" /> 48 <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" />
49 <param name="kmer" type="integer" value="32" label="K-mer" help="K-mer size to use (default: 32)" /> 49 <param name="kmer" type="integer" value="32" label="K-mer" help="K-mer size to use (default: 32)" />
50 <param name="ukmer" type="integer" value="0" label="Unique K-mer" help="approximate number of unique kmers in the input set (default: 0)" /> 50 <param name="ukmer" type="integer" value="0" label="Unique K-mer" help="approximate number of unique kmers in the input set (default: 0)" />
51 <param name="num_table" type="integer" value="0" label="Number of tables" help="number of tables to use (default: False)" /> 51 <param name="num_table" type="integer" value="0" label="Number of tables" help="number of tables to use (default: False)" />