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comparison kwip.xml @ 8:f99fa69fe0d5 draft

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planemo upload
author jowong
date Thu, 22 Nov 2018 07:39:58 -0500
parents 1850de9baad0
children 9e7f04e98343
comparison
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7:1850de9baad0 8:f99fa69fe0d5
1 <tool id="kwip" name="kwip" version="1.1.6"> 1 <tool id="kwip" name="kwip" version="1.1.7">
2 <description>Calculates k-mer weighted inner product, a de novo estimator of genetic similarity</description> 2 <description>Calculates k-mer weighted inner product, a de novo estimator of genetic similarity</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.0">kwip</requirement> 4 <requirement type="package" version="0.2.0">kwip</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
8 kwip 8 kwip
9 -t $advanced.thread 9 -t $advanced.thread
10 -k kwip.kernel 10 -k kwip.kernel
11 -d kwip.dist 11 -d kwip.dist
12 $advanced.unweighted 12 $advanced.unweighted
13 #if str( $advanced.calc ) == "True"
14 -w $advanced.weight -C
15 #end if
16 #for $input in $inputs# $(basename "$input.element_identifier" .fastq).ct.gz #end for# 13 #for $input in $inputs# $(basename "$input.element_identifier" .fastq).ct.gz #end for#
17 #for $input in $inputs# && rm $(basename "$input.element_identifier" .fastq).ct.gz #end for# 14 #for $input in $inputs# && rm $(basename "$input.element_identifier" .fastq).ct.gz #end for#
18 ]]></command> 15 ]]></command>
19 <inputs> 16 <inputs>
20 <param name="inputs" format="data" type="data_collection" label="inputs" help="Specify dataset with hashed reads"/> 17 <param name="inputs" format="data" type="data_collection" label="inputs" help="Specify dataset with hashed reads"/>
21 <section name="advanced" title="Advanced options" expanded="false"> 18 <section name="advanced" title="Advanced options" expanded="false">
22 <param type="boolean" argument="--unweighted" label="Unweighted Inner Product" checked="false" truevalue="--unweighted" falsevalue="" help="Use the unweighted inner proudct kernel. (default: False)"/> 19 <param type="boolean" argument="--unweighted" label="Unweighted Inner Product" checked="false" truevalue="--unweighted" falsevalue="" help="Use the unweighted inner proudct kernel. (default: False)"/>
23 <param type="boolean" name="calc" label="Calculate only the bin weight vector, not kernel matrix." help="Calculate only the bin weight vector, not kernel matrix with bin weight vector file" truevalue="True" falsevalue="False" checked="false" />
24 <param type="data" name="weight" label="Bin weight vector file" help="Bin weight vector file (input, or output w/ -C)." />
25 <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" /> 20 <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" />
26 21
27 </section> 22 </section>
28 </inputs> 23 </inputs>
29 <outputs> 24 <outputs>