diff hicTransform.xml @ 0:369f6cb43a86 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicTransform.xml	Sat Dec 30 09:19:19 2017 -0500
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+<tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>transforms a matrix to a obs_exp, pearson and covariance matrix</description>
+    <macros>
+        <token name="@BINARY@">hicTransform</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+
+
+        hicTransform --matrix '$matrix_h5_cooler'
+        --method all
+
+        #if $outputFormat == 'h5'
+            --outFileName matrix.h5
+        #elif $outputFormat == 'cool'
+            --outFileName matrix.cool
+        #end if
+
+]]>
+    </command>
+    <inputs>
+        <expand macro='matrix_h5_cooler_macro' />
+        <param name='outputFormat' type='select' label="Output file format">
+            <option value='h5'>HiCExplorer format</option>
+            <option value="cool">cool</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="obs_exp_h5" from_work_dir="obs_exp_matrix.h5" format="h5">
+            <filter>outputFormat == 'h5'</filter>
+        </data>
+        <data name="pearson_h5" from_work_dir="pearson_matrix.h5" format="h5">
+            <filter>outputFormat == 'h5'</filter>
+        </data>
+        <data name="covariance_h5" from_work_dir="covariance_matrix.h5" format="h5">
+            <filter>outputFormat == 'h5'</filter>
+        </data>
+        <data name="obs_exp_cool" from_work_dir="obs_exp_matrix.cool" format="cool">
+            <filter>outputFormat == 'cool'</filter>
+        </data>
+        <data name="pearson_cool" from_work_dir="pearson_matrix.cool" format="cool">
+            <filter>outputFormat == 'cool'</filter>
+        </data>
+        <data name="covariance_cool" from_work_dir="covariance_matrix.cool" format="cool">
+            <filter>outputFormat == 'cool'</filter>
+        </data>
+
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
+            <param name="outputFormat" value="h5" />
+            <output name="obs_exp_h5" file="obs_exp_small_50kb.h5" ftype="h5" compare="sim_size"/>
+            <output name="pearson_h5" file="pearson_small_50kb.h5" ftype="h5" compare="sim_size"/>
+            <output name="covariance_h5" file="covariance_small_50kb.h5" ftype="h5" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
+            <param name="outputFormat" value="cool" />
+            <output name="obs_exp_cool" file="obs_exp_small_50kb.cool" ftype="cool" compare="sim_size"/>
+            <output name="pearson_cool" file="pearson_small_50kb.cool" ftype="cool" compare="sim_size"/>
+            <output name="covariance_cool" file="covariance_small_50kb.cool" ftype="cool" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Transformation of matrix for plotting
+=====================================
+`hicTransform` computes three matrices: an observed/expected matrix based on it a
+pearson correlation matrix and based on it a covariance matrix. These three matrices
+can be used with `hicPlotMatrix` for an A / B compartment analysis.
+
+Input
+-----
+- the matrix to be transformed
+
+Parameters
+__________
+- Output file format: h5 or cool
+
+Output
+------
+- observed/expected matrix
+- pearson correlation matrix 
+- covariance matrix.
+
+| For more information about HiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+]]></help>
+    <expand macro="citations" />
+</tool>