diff hicTransform.xml @ 9:3f529510975e draft

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

--- a/hicTransform.xml	Mon Dec 16 15:41:36 2019 -0500
+++ b/hicTransform.xml	Wed Feb 05 19:55:59 2020 -0500
@@ -10,7 +10,16 @@
         ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
         @BINARY@ --matrix 'matrix.$matrix_h5_cooler.ext'
         --method $method_selector
+        #if $ligation_factor:
+            $ligation_factor
+        #end if
+        $perChromosome
+        #set chroms = ' '.join([ '\'' + str($var.chromosome) + '\'' for $var in $chromosomeOrder ])
+        #if chroms:
+            --chromosomes $chroms
+        #end if
         --outFileName 'matrix.$matrix_h5_cooler.ext'
+
         && mv 'matrix.$matrix_h5_cooler.ext' matrix
 ]]>
     </command>
@@ -18,12 +27,19 @@
         <expand macro='matrix_h5_cooler_macro' />
         <param name="method_selector" type="select" label="Choose method to apply">
                 <option value="obs_exp" selected="True">obs / exp</option>
-                <option value="obs_exp_norm">obs / exp (Homer norm)</option>
+                <option value="obs_exp_lieberman">obs / exp (Lieberman-Aiden 2009)</option>
                 <option value="obs_exp_non_zero">obs / exp (exclude non-zero from exp)</option>
                 <option value="pearson">pearson</option>
                 <option value="covariance">covariance</option>
         </param>
-
+        <param name='ligation_factor' type='boolean' truevalue='--ligation_factor' falsevalue="" checked="false" label='Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation'/>
+        <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false"
+            label="Computation per chromosome" />
+        <repeat name="chromosomeOrder" min="0" title="Chromosomes to include int the computation" >
+            <param name="chromosome" type="text" >
+                <validator type="empty_field" />
+            </param>
+        </repeat>
     </inputs>
     <outputs>
         <data name="matrix_out" from_work_dir="matrix" format="cool" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: $method_selector">
@@ -35,7 +51,18 @@
     <tests>
         <test>
             <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
-            <param name='method_selector' value='obs_exp_norm'/>
+            <param name='method_selector' value='obs_exp_lieberman'/>
+            <output name="matrix_out" ftype="h5">
+                <assert_contents>
+                    <has_h5_keys keys='intervals,matrix'/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
+            <param name='method_selector' value='obs_exp_lieberman'/>
+            <param name='ligation_factor' value='True'/>
+
             <output name="matrix_out" ftype="h5">
                 <assert_contents>
                     <has_h5_keys keys='intervals,matrix'/>