Mercurial > repos > saket-choudhary > inchlib_clust
view inchlib_clust/inchlib_clust.xml @ 0:60f93f839759 draft default tip
Uploaded
author | saket-choudhary |
---|---|
date | Tue, 07 Oct 2014 19:35:50 -0400 |
parents | |
children |
line wrap: on
line source
<tool id="inchlib_clust" name="INCHlib" version="1.0.0" hidden="false"> <requirements> <requirement type="package" version="3.5.0">blas</requirement> <requirement type="package" version="1.7">numpy</requirement> <requirement type="package" version="0.12">scipy</requirement> <requirement type="package" version="0.15">scikit-learn</requirement> <requirement type="package" version="1.1.13">fastcluster</requirement> <requirement type="python-module">numpy</requirement> <requirement type="python-module">scipy</requirement> <requirement type="python-module">scikit-learn</requirement> <requirement type="python-module">fastcluster</requirement> </requirements> <description>Performs data clustering for input to InCHlib.js</description> <command interpreter="python"> inchlib_clust.py $input -o $output --row_distance $row_distance --row_linkage $row_linkage --column_distance $column_distance --column_linkage $column_linkage --axis $axis --datatype $datatype --data_delimiter $data_delimiter #if $data_header.data_header_present == "yes" --data_header #end if #if $metadata_option.metadata_present == "yes" --metadata $metadata_option.metadata --metadata_delimiter $metadata_option.metadata_delimiter #if $metadata_option.metadata_header.metadata_header_present == "yes" --metadata_header #end if #if $metadata_option.metadata_compress_option.should_compress_metadata == "yes" --metadata_compressed_value $metadata_option.metadata_compressed_value #end if #end if #if $data_compress_option.should_compress_data == "yes" --data_compressed_value $data_compressed_value #end if #if $should_normalize == "yes" --normalize #end if </command> <inputs> <param format="text" name="input" type="data" label="Input File" /> <param name="row_distance" type="select" label="Row Distance Method" help="Set the distance to use for clustering rows"> <option value="braycurtis">braycurtis</option> <option value="canberra">canberra</option> <option value="chebyshev">chebyshev</option> <option value="cityblock">cityblock</option> <option value="correlation">correlation</option> <option value="cosine">cosine</option> <option value="euclidean" selected="true">euclidean</option> <option value="mahalanobis">mahalanobis</option> <option value="minkowski">minkowski</option> <option value="seuclidean">seuclidean</option> <option value="sqeuclidean">sqeuclidean</option> <option value="dice">dice</option> <option value="hamming">hamming</option> <option value="jaccard">jaccard</option> <option value="kulsinski">kulsinski</option> <option value="matching">matching</option> <option value="rogerstanimoto">rogerstanimoto</option> <option value="russellrao">russellrao</option> <option value="sokalmichener">sokalmichener</option> <option value="sokalsneath">sokalsneath</option> <option value="yule">yule</option> </param> <param name="row_linkage" type="select" label="Row Linkage Method" help="Set the linkage to use for clustering rows"> <option value="single">single</option> <option value="complete">complete</option> <option value="average">average</option> <option value="centroid">centroid</option> <option value="ward">ward</option> <option value="median">median</option> <option value="weighted">weighted</option> <option value="ward" selected="true">ward</option> <option value="centroid">centroid</option> </param> <param name="column_distance" type="select" label="Column Distance Method" help="Set the distance to use for clustering columns"> <option value="braycurtis">braycurtis</option> <option value="canberra">canberra</option> <option value="chebyshev">chebyshev</option> <option value="cityblock">cityblock</option> <option value="correlation">correlation</option> <option value="cosine">cosine</option> <option value="euclidean" selected="true">euclidean</option> <option value="mahalanobis">mahalanobis</option> <option value="minkowski">minkowski</option> <option value="seuclidean">seuclidean</option> <option value="sqeuclidean">sqeuclidean</option> <option value="dice">dice</option> <option value="hamming">hamming</option> <option value="jaccard">jaccard</option> <option value="kulsinski">kulsinski</option> <option value="matching">matching</option> <option value="rogerstanimoto">rogerstanimoto</option> <option value="russellrao">russellrao</option> <option value="sokalmichener">sokalmichener</option> <option value="sokalsneath">sokalsneath</option> <option value="yule">yule</option> </param> <param name="column_linkage" type="select" label="Column Linkage" help="Set the linkage to use for clustering columns"> <option value="single">single</option> <option value="complete">complete</option> <option value="average">average</option> <option value="centroid">centroid</option> <option value="ward">ward</option> <option value="median">median</option> <option value="weighted">weighted</option> <option value="ward" selected="true">ward</option> <option value="centroid">centroid</option> </param> <param name="axis" type="select" label="Clustering Axis"> <option value="row" selected="true">row</option> <option value="both">both</option> </param> <param name="datatype" type="select" label="Type Of Data"> <option value="numeric" selected="true">numeric</option> <option value="binary">binary</option> </param> <param name="data_delimiter" type="select" label="Data Delimiter"> <option value="\t">tab</option> <option value=",">comma</option> <option value=";">semicolon</option> </param> <conditional name="data_header"> <param name="data_header_present" type="select" label="First row of file is header"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> </conditional> <conditional name="data_compress_option"> <param name="should_compress_data" type="select" label="Compress Rows"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="yes"> <param name="data_compressed_value" type="select"> <option value="median" selected="true">median</option> <option value="mean">mean</option> </param> </when> </conditional> <param name="should_normalize" type="select" label="Normalise"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <conditional name="metadata_option"> <param name="metadata_present" type="select" label="Metadata Input"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="yes"> <param name="metadata" type="data" format="text" label="Metadata File"/> <conditional name="metadata_header"> <param name="metadata_header_present" type="select" label="Metadata Header Present?"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> </conditional> <param name="metadata_delimiter" type="select" label="Metadata Delimiter"> <option value="\t">tab</option> <option value=",">comma</option> <option value=";">semicolon</option> </param> <conditional name="metadata_compress_option"> <param name="should_compress_metadata" type="select" label="Compress Metadata Rows?"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="yes"> <param name="metadata_compressed_value" type="select"> <option value="median" selected="true">median</option> <option value="mean">mean</option> <option value="frequency">frequency</option> </param> </when> </conditional> </when> </conditional> </inputs> <outputs> <data format="json" name="output" label="${tool.name} on ${on_string}: output" /> </outputs> <tests> <test> <param name="input" value="inchlib_input1.csv"/> <param name="row_distance" value="euclidean"/> <param name="row_linkage" value="ward"/> <param name="column_distance" value="euclidean"/> <param name="column_linkage" value="ward"/> <param name="axis" value="row" /> <param name="datatype" value="numeric" /> <param name="data_delimiter" value="," /> <param name="data_header_present" value="yes" /> <param name="should_compress_data" value="no" /> <param name="should_normalize" value="no" /> <param name="metadata_present" value="yes" /> <param name="metadata" value="inchlib_input_metadata.csv" /> <param name="metadata_delimiter" value="," /> <param name="metadata_header_present" value="yes" /> <output name="output" file="inchlib_output.json" ftype="json" /> </test> </tests> <help> **What it does** Performs data clustering and prepares input data for InCHlib. </help> </tool>