diff hicTransform.xml @ 14:9667ab8e2085 draft

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

--- a/hicTransform.xml	Fri Dec 11 21:07:29 2020 +0000
+++ b/hicTransform.xml	Tue Mar 16 15:20:25 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hictransform" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>transform a matrix to obs/exp, pearson and covariance matrices</description>
     <macros>
         <token name="@BINARY@">hicTransform</token>
@@ -26,46 +26,45 @@
     <inputs>
         <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>
-                <option value="obs_exp_non_zero">obs / exp (exclude non-zero from exp)</option>
-                <option value="pearson">pearson</option>
-                <option value="covariance">covariance</option>
+            <option value="obs_exp" selected="True">obs / exp</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" >
+        <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">
                 <validator type="empty_field" />
+                <validator type="expression" message="Only alphanumeric characters and the underscore can be used in chromosome names">value.replace('_', '').isalnum()</validator>
             </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">
             <change_format>
-                <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/>
+                <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
             </change_format>
         </data>
     </outputs>
     <tests>
         <test>
-            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
-            <param name='method_selector' value='obs_exp_lieberman'/>
+            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
+            <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="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'/>
+                    <has_h5_keys keys='intervals,matrix' />
                 </assert_contents>
             </output>
         </test>
@@ -97,6 +96,6 @@
 
 .. _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>