diff hicCompartmentalization.xml @ 1:c6f32406aa3c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicCompartmentalization.xml	Wed Feb 05 19:49:53 2020 -0500
@@ -0,0 +1,95 @@
+<tool id="hicexplorer_hiccompartmentspolarization" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>compute pairwise correlations between multiple Hi-C contact matrices</description>
+    <macros>
+        <token name="@BINARY@">hicCompartmentalization</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+
+        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
+            ln -s '$m' '${counter}_matrix.$m.ext' &&
+        #end for
+        #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
+       
+        @BINARY@
+
+            --obsexp_matrices $m
+
+            --pca '$pca'
+            --quantile $quantile
+
+            #if $set_offset_value:
+                #set $offset_array = $set_offset_value.split(' ')
+                #set $offset = ' '.join([ '%s' % int($value) for $value in $offset_array ])
+                --offset $offset
+            #end if
+            --outliers $outliers
+            --outputFileName plot.$image_file_format
+
+        && mv plot.$image_file_format plot
+]]>
+    </command>
+    <inputs>
+        <expand macro="matrix_h5_cooler_multiple_macro" />
+        <param name='pca'  type="data" format="bedgraph" label="Eigenvector file" help='A PCA vector as a bedgraph file with 
+                                no header. In case of several matrices with 
+                                 different conditions, ie. control
+                                treatment, the PCA of control can be 
+                                used. Note that only one PCA can be provided.'/>
+        <param name='quantile'  type="integer" label="Quantile" help='The number of to be used quantiles.' value="30"/>
+        <param name='outliers'  type="float"  label="Outliers" help='The number of outliers to be removed.' value="0.0"/>
+        <param name="set_offset_value" type="text" value="" label="Offset values" optional='True'/>
+      
+        <param name="image_file_format" type="select" label="Image output format">
+            <option value="png" selected="True">png</option>
+            <option value="svg">svg</option>
+            <option value="pdf">pdf</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
+            <change_format>
+                <when input="image_file_format" value="svg" format="svg" />
+                <when input="image_file_format" value="pdf" format="pdf" />
+            </change_format>
+        </data>
+        <data name='output_matrix' from_work_dir='output_matrix.npz' format='binary' label='Output .npz file includes all the generated matrices'>
+            <filter>outputMatrix == '--outputMatrix output_matrix.npz'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/>
+            <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
+            <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/>
+            <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
+            <param name="quantile" value='30'/>
+            <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/>
+            <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
+            <param name="outliers" value='1.0'/>
+            <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Comparmentalization
+===================
+
+**hicCompartmentalization** rearranges the average interaction frequencies using the first PC values to represent the global compartmentalization signal.
+To our knowledge this has been first introduced and implemented by Wibke Schwarzer et al. 2017 (Nature. 2017 Nov 2; 551(7678): 51–56)
+
+
+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>