diff hicTransform.xml @ 4:d5bf6e7d3800 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8

--- a/hicTransform.xml	Wed Mar 07 03:41:00 2018 -0500
+++ b/hicTransform.xml	Fri Apr 27 03:34:37 2018 -0400
@@ -1,5 +1,5 @@
 <tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.0">
-    <description>transforms a matrix to a obs_exp, pearson and covariance matrix</description>
+    <description>transform a matrix to obs/exp, pearson and covariance matrices</description>
     <macros>
         <token name="@BINARY@">hicTransform</token>
         <import>macros.xml</import>
@@ -25,19 +25,19 @@
 
     </inputs>
     <outputs>
-        <data name="obs_exp" from_work_dir="obs_exp_matrix" format="h5">
+        <data name="obs_exp" from_work_dir="obs_exp_matrix" format="h5" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Observed/Expected matrix">
             <change_format>
-                <when input="outputFormat" value="cool" format="cool" />
+                <when input="outputFormat" value="cool" format="cool"/>
             </change_format>
         </data>
-        <data name="pearson" from_work_dir="pearson_matrix" format="h5">
+        <data name="pearson" from_work_dir="pearson_matrix" format="h5" label="${tool.name}  on ${matrix_h5_cooler.name} [${on_string}]: Pearson matrix">
             <change_format>
-                <when input="outputFormat" value="cool" format="cool" />
+                <when input="outputFormat" value="cool" format="cool"/>
             </change_format>
         </data>
-        <data name="covariance" from_work_dir="covariance_matrix" format="h5">
+        <data name="covariance" from_work_dir="covariance_matrix" format="h5" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Covariance matrix">
             <change_format>
-                <when input="outputFormat" value="cool" format="cool" />
+                <when input="outputFormat" value="cool" format="cool"/>
             </change_format>
         </data>
 
@@ -61,27 +61,28 @@
     <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.
+
+**hicTransform** computes three matrices based on one Hi-C contact matrix as input based on the methods determined by `Lieberman-Aiden et al. (2009)`_:
 
-Input
------
-- the matrix to be transformed
+- An **observed/expected matrix** obtained "by dividing each entry in the contact matrix by the genome-wide average contact probability for loci at that genomic distance" (`Lieberman-Aiden et al. (2009)`_). This transformation allows to better assess long range interactions.
+- A **Pearson correlation matrix** obtained by computing the Pearson correlation between each bin based on observed/expected values. This matrix transformation allows to better identify the bins that are entering in contact together, or not, at long ranges, and thus helps defining compartments in the nucleus (``hicPCA``).
+- A **covariance matrix**, which is used as a basis for the Principal Component Analysis (PCA) to compute the eigenvectors outputed by **hicTransform**.
 
-Parameters
-__________
-- Output file format: h5 or cool
+These three matrices can be used with ``hicPlotMatrix`` or ``hicPlotTADs`` for a visualization of the A / B compartment analysis.
+
+_________________
 
 Output
 ------
-- observed/expected matrix
-- pearson correlation matrix 
-- covariance matrix.
+
+From one Hi-C contact matrix, **hicTransform** outputs the observed/expected, Pearson correlation and covariance matrices.
+
+_________________
 
 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+.. _`Lieberman-Aiden et al. (2009)`: https://dx.doi.org/10.1126%2Fscience.1181369
 ]]></help>
     <expand macro="citations" />
 </tool>