diff kwip.xml @ 0:6c38443b46ac draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kwip.xml	Thu Nov 22 09:47:44 2018 -0500
@@ -0,0 +1,61 @@
+<tool id="kwip" name="kwip" version="1.2.9">
+    <description>Calculates k-mer weighted inner product, a de novo estimator of genetic similarity</description>
+    <requirements>
+        <requirement type="package" version="0.2.0">kwip</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #for $input in $inputs# cp $input $(input.element_identifier).ct.gz && #end for# 
+        kwip 
+        -t $advanced.thread 
+        -k kwip.kernel 
+        -d kwip.dist 
+        #for $input in $inputs# $(input.element_identifier).ct.gz #end for#
+        #for $input in $inputs# && rm $(input.element_identifier).ct.gz #end for#
+    ]]></command>
+    <inputs>
+        <param name="inputs" format="data" type="data_collection" label="inputs" help="Specify dataset with hashed reads"/>
+        <section name="advanced" title="Advanced options" expanded="false">
+            <param type="boolean" argument="--unweighted" label="Unweighted Inner Product" checked="false" truevalue="--unweighted" falsevalue="" help="Use the unweighted inner proudct kernel. (default: False)"/>
+            <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" />
+
+        </section>
+    </inputs>
+    <outputs>
+        <data name="kwip_kernel" label="kWip kernel" format="txt" type="data" from_work_dir="kwip.kernel"/>
+        <data name="kwip_distance" label="kWip distance" format="txt" type="data" from_work_dir="kwip.dist"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+        usage: USAGE: kwip [options] hashes
+
+	kWip Options.
+
+	optional arguments:
+          -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 = {Murray, Kevin},
+  year = {2015},
+  title = {kWIP},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/kdmurray91/kWIPE},
+}</citation>
+    </citations>
+</tool>