# HG changeset patch
# User jowong
# Date 1542628501 18000
# Node ID 66d91eade17a120d49241a25291b7904947e7fb8
# Parent  39519109479fd88e501c4e94e85b9faad2c47655
planemo upload

diff -r 39519109479f -r 66d91eade17a kwip.xml
--- a/kwip.xml	Mon Nov 19 04:19:54 2018 -0500
+++ b/kwip.xml	Mon Nov 19 06:55:01 2018 -0500
@@ -1,48 +1,65 @@
-<tool id="kwip" name="kwip" version="1.1.0">
+<tool id="kwip" name="kwip" version="1.1.1">
     <description>Calculates CNV of genomic data based on template</description>
     <requirements>
         <requirement type="package" version="0.2.0">kwip</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        kwip -h
+        kwip 
+        -t $advanced.thread 
+        -k kwip.kernel 
+        -d kwip.dist 
+        $advanced.unweighted
+        #if str( $advanced.calc ) == "True"
+            -w $advanced.weight -C
+        #end if 
+        #for $path in $paths# $path #end for#
     ]]></command>
     <inputs>
-        <param type="data" name="input1" format="txt" />
+        <param name="input" format="data" type="data_collection" label="input" help="Specify dataset with hashed reads"/>
+        <section name="advanced" title="Advanced options" expanded="false">
+            <param type="boolean" argument="--unweighted" label="Small count" checked="false" truevalue="--unweighted" falsevalue="" help="Use the unweighted inner proudct kernel. (default: False)"/>
+            <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" />
+            <param type="data" name="weight" label="Bin weight vector file" help="Bin weight vector file (input, or output w/ -C)." />
+            <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" />
+
+        </section>
     </inputs>
     <outputs>
-        <data name="output1" format="txt" />
+        <data name="kwip_kernel" label="kWip kernel" format="data" from_work_dir="kwip.kernel"/>
+        <data name="kwip_distance" label="kWip distance" format="data" from_work_dir="kwip.dist"/>
     </outputs>
     <tests>
-        <test>
-            <param name="input1" value="prince_input.txt"/>
-            <output name="output1" file="prince_output.txt"/>
-        </test>
     </tests>
     <help><![CDATA[
-        usage: prince [-h] [-bo BOOST_OUTPUT] [-to TARGET_OUTPUT] [-tmp TEMPLATES] [-tf TARGET_FILE] [-bf BOOSTING_FILE] [-k K] [-cn COPYNUMBER]
+        usage: USAGE: kwip [options] hashes
 
-	Prince Options.
+	kWip Options.
 
 	optional arguments:
-	  -h, --help            Show this help message and exit
-	  -bo, --boost_output   Output file for training data / training data used to predict copy numbers for queries
-          -to, --target_output  Output file for query copy number predictions
-          -tmp, --templates     VNTR templates. Default is for M.TB
-          -tf, --target_file    Target genome names in a text file
-          -bf, --boosting_file  Training genome file names in a text file
-          -k, --k               Kmer size used during read recruitment
-          -cn, --copynumber     Copy number used for training genome
+          -t, --threads       Number of threads to utilise. [default N_CPUS]
+          -k, --kernel        Output file for the kernel matrix. [default None]
+          -d, --distance      Output file for the distance matrix. [default stdout]
+          -U, --unweighted    Use the unweighted inner proudct kernel. [default off]
+          -w, --weights       Bin weight vector file (input, or output w/ -C).
+          -C, --calc-weights  Calculate only the bin weight vector, not kernel matrix.
+          -h, --help          Print this help message.
+          -V, --version       Print the version string.
+          -v, --verbose       Increase verbosity. May or may not acutally do anything.
+          -q, --quiet         Execute silently but for errors.
+
+          Each sample's oxli Countgraph should be specified after arguments:
+          kwip [options] sample1.ct sample2.ct ... sampleN.ct
 
     ]]></help>
     <citations>
         <citation type="bibtex">
 @misc{githubPythonPRINCE,
-  author = {Booth, Julian},
-  year = {2018},
-  title = {PythonPRINCE},
+  author = {Murray, Kevin},
+  year = {2015},
+  title = {kWIP},
   publisher = {GitHub},
   journal = {GitHub repository},
-  url = {https://github.com/WGS-TB/PythonPRINCE},
+  url = {https://github.com/kdmurray91/kWIPE},
 }</citation>
     </citations>
 </tool>