diff hicPCA.xml @ 9:3ed8e85f4f4c draft

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

--- a/hicPCA.xml	Mon Dec 16 14:33:42 2019 -0500
+++ b/hicPCA.xml	Wed Feb 05 19:41:11 2020 -0500
@@ -14,8 +14,12 @@
         --outputFileName pca1.$outputFormat pca2.$outputFormat
         --format $outputFormat
 
-        #if $norm:
-            $norm
+        #if $ligation_factor:
+            $ligation_factor
+        #end if
+
+        #if $ignoreMaskedBins:
+            $ignoreMaskedBins
         #end if
 
         #if $extra_track_conditional.extra_track_selection == 'gene_density':
@@ -54,7 +58,8 @@
 
         <expand macro="chromosome_list" />
 
-        <param name='norm' type='boolean' truevalue='--norm' label='Use different expected value computation'/>
+        <param name='ligation_factor' type='boolean' truevalue='--ligation_factor' label='Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation'/>
+        <param name='ignoreMaskedBins' type='boolean' truevalue='--ignoreMaskedBins' label='This option removes the masked bins before the PCA is computed'/>
 
         <conditional name="extra_track_conditional">
             <param name='extra_track_selection' label='Extra track type' type='select'>
@@ -116,6 +121,30 @@
             <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
         </test>
         <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
+            <param name="outputFormat" value="bigwig" />
+            <param name="ligation_factor" value="True" />
+
+            <conditional name="extra_track_conditional">
+                <param name="extra_track_selection" value=""/>
+            </conditional>
+
+            <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
+            <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
+        </test>
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
+            <param name="outputFormat" value="bigwig" />
+            <param name="ignoreMaskedBins" value="True" />
+
+            <conditional name="extra_track_conditional">
+                <param name="extra_track_selection" value=""/>
+            </conditional>
+
+            <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='60000'/>
+            <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='60000'/>
+        </test>
+        <test>
             <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
             <param name="outputFormat" value="bigwig" />
             <conditional name="extra_track_conditional">
@@ -140,7 +169,6 @@
             <conditional name="extra_track_conditional">
                 <param name="extra_track_selection" value=""/>
             </conditional>
-            <param name='norm' value='True'/>
             <param name='pearsonMatrix' value='True'/>
             <param name='obsexpMatrix' value='True'/>