diff hicNormalize.xml @ 6:05257e5d5016 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"

--- a/hicNormalize.xml	Fri Dec 11 20:58:36 2020 +0000
+++ b/hicNormalize.xml	Tue Mar 16 15:29:18 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>normalizes a matrix to norm range or smallest read count</description>
     <macros>
         <token name="@BINARY@">hicNormalize</token>
@@ -28,65 +28,76 @@
 ]]>
     </command>
     <inputs>
-        <expand macro='matrix_h5_cooler_multiple_macro'/>
+        <expand macro='matrix_h5_cooler_multiple_macro' />
         <conditional name="normalize_conditional">
             <param name='normalize' type='select' label='Normalize matrices'>
                 <option value='norm_range'>0 to 1 range</option>
                 <option value='smallest'>Smallest read count</option>
                 <option value='multiplicative'>Multiply by value</option>
             </param>
-            <when value='norm_range'/>
-            <when value='smallest'/>
+            <when value='norm_range' />
+            <when value='smallest' />
             <when value='multiplicative'>
-                <param name="multiplicativeValue" type="float" value="1.0" label="Multiplicative value"/>
+                <param name="multiplicativeValue" type="float" value="1.0" label="Multiplicative value" />
             </when>
         </conditional>
-        <param name="zero_threshold_value" type="float" value="1.0" optional='True' label="Set values below this threshold to zero"/>
+        <param name="zero_threshold_value" type="float" value="1.0" optional='True' label="Set values below this threshold to zero" />
     </inputs>
     <outputs>
         <data format='cool' name="normalize_matrix">
-            <discover_datasets pattern="__name_and_ext__" directory="output"  visible="true"/>
+            <discover_datasets pattern="__name_and_ext__" directory="output" visible="true" />
             <change_format>
-                <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5"/>
+                <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5" />
             </change_format>
         </data>
     </outputs>
     <tests>
         <test>
-            <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool"/>
-            <param name='normalize' value='norm_range'/>
+            <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool" />
+            <param name='normalize' value='norm_range' />
             <output name="normalize_matrix">
                 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
-                    <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
+                    <assert_contents>
+                        <has_h5_keys keys="bins,chroms,indexes,pixels" />
+                    </assert_contents>
                 </discovered_dataset>
             </output>
         </test>
         <test>
-            <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool"/>
-            <param name='normalize' value='smallest'/>
+            <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool" />
+            <param name='normalize' value='smallest' />
             <output name="normalize_matrix">
                 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
-                    <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
+                    <assert_contents>
+                        <has_h5_keys keys="bins,chroms,indexes,pixels" />
+                    </assert_contents>
                 </discovered_dataset>
                 <discovered_dataset designation="1_norm_small_test_matrix" ftype="cool">
-                    <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
+                    <assert_contents>
+                        <has_h5_keys keys="bins,chroms,indexes,pixels" />
+                    </assert_contents>
                 </discovered_dataset>
             </output>
         </test>
         <test>
-            <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/>
-            <param name='normalize' value='smallest'/>
+            <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5" />
+            <param name='normalize' value='smallest' />
             <output name="normalize_matrix">
                 <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5">
-                    <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents>
+                    <assert_contents>
+                        <has_h5_keys keys="intervals,matrix" />
+                    </assert_contents>
                 </discovered_dataset>
                 <discovered_dataset designation="1_norm_small_test_matrix" ftype="h5">
-                    <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents>
+                    <assert_contents>
+                        <has_h5_keys keys="intervals,matrix" />
+                    </assert_contents>
                 </discovered_dataset>
             </output>
         </test>
     </tests>
     <help><![CDATA[
+
 Normalization of matrices
 =========================
 
@@ -105,6 +116,6 @@
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
 .. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369
-]]></help>
+]]>    </help>
     <expand macro="citations" />
 </tool>