diff hicTransform.xml @ 16:f36828ebdc54 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9

--- a/hicTransform.xml	Tue Jan 10 18:44:33 2023 +0000
+++ b/hicTransform.xml	Wed Oct 18 10:24:58 2023 +0000
@@ -24,7 +24,7 @@
 ]]>
     </command>
     <inputs>
-        <expand macro='matrix_h5_cooler_macro' />
+        <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_lieberman">obs / exp (Lieberman-Aiden 2009)</option>
@@ -32,7 +32,7 @@
             <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 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 in the computation">
             <param name="chromosome" type="text">
@@ -51,20 +51,20 @@
     <tests>
         <test>
             <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
-            <param name='method_selector' value='obs_exp_lieberman' />
+            <param name="method_selector" value="obs_exp_lieberman" />
             <output name="matrix_out" ftype="h5">
                 <assert_contents>
-                    <has_h5_keys keys='intervals,matrix' />
+                    <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' />
+            <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' />
+                    <has_h5_keys keys="intervals,matrix" />
                 </assert_contents>
             </output>
         </test>
@@ -95,7 +95,7 @@
 | 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://doi.org/10.1126/science.1181369
+.. _`Lieberman-Aiden et al. (2009)`: https://pubmed.ncbi.nlm.nih.gov/19815776/
 ]]>    </help>
     <expand macro="citations" />
 </tool>