diff macros.xml @ 7:554e8a6cec27 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788

--- a/macros.xml	Tue Jan 10 18:19:18 2023 +0000
+++ b/macros.xml	Mon Jul 01 18:52:21 2024 +0000
@@ -1,7 +1,8 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@TOOL_VERSION@">3.6</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">3.7.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">23.0</token>
     <token name="@USE_RANGE@">
         #if $use_range.select_use_range == "yes_use_range":
             --range $use_range.range_min:$use_range.range_max
@@ -37,7 +38,8 @@
 
     <xml name="citations">
         <citations>
-            <citation type="doi">10.5281/zenodo.1133705</citation>
+            <citation type="doi">10.1093/nar/gkaa220</citation>
+            <citation type="doi">10.1093/nar/gky504</citation>
             <yield />
         </citations>
     </xml>
@@ -247,7 +249,7 @@
         #set $matrices = []
         #set $mlabels = []
         #for $counter, $i in enumerate($input_files):
-            ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext'; 
+            ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext';
             #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter,  $i.matrix.ext))
 
             #if str($i.mlabel.value) != "":
@@ -348,6 +350,10 @@
     <xml name='matrix_h5_cooler_multiple_macro'>
         <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" />
     </xml>
+
+    <xml name='matrix_cooler_multiple_macro'>
+        <param name='matrix_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Hi-C matrix" />
+    </xml>
     <xml name='convertFormat_single_macro'>
         <conditional name="inputFormat_conditional">
             <param name="inputFormat_selector" type="select" label="Choose input file type">
@@ -356,6 +362,8 @@
                 <option value="optionHic">hic</option>
                 <option value="optionHomer">Homer</option>
                 <option value="optionHicpro">HiCPro</option>
+                <option value="option2Dtext">2D-text</option>
+
             </param>
             <when value="optionCool">
                 <expand macro='matrix_h5_cooler_macro' />
@@ -377,9 +385,17 @@
                 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' />
             </when>
             <when value="optionHicpro">
-                <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' />
+                <param name='matrixHicpro' type='data' format='txt' label='.hicpro matrix' />
                 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' />
             </when>
+            <when value="option2Dtext">
+                <param name='matrix2Dtext' type='data' format='txt' label='A 2D text matrix' />
+
+                <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
+                    <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
+                </param>
+                <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
+            </when>
         </conditional>
     </xml>
 
@@ -390,6 +406,9 @@
                 <option value="optionH5">h5</option>
                 <option value="optionHomer">Homer</option>
                 <option value="optionHicpro">HiCPro</option>
+                <option value="option2Dtext">2D-text</option>
+
+
             </param>
             <when value="optionCool">
                 <expand macro='matrix_h5_cooler_multiple_macro' />
@@ -408,6 +427,14 @@
                 <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' />
                 <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' />
             </when>
+            <when value="option2Dtext">
+                <param name='matrix2Dtext' type='data' format='txt' multiple="true" label='A 2D text matrix' />
+
+                <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
+                    <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
+                </param>
+                <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
+            </when>
         </conditional>
     </xml>
     <xml name='convertFormat_single_output_macro'>
@@ -418,6 +445,8 @@
                 <option value="h5">h5</option>
                 <option value="homer">Homer</option>
                 <option value="ginteractions">ginteractions</option>
+                <option value="hicpro">hicpro</option>
+
             </param>
             <when value="cool">
                 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' />
@@ -426,6 +455,7 @@
             <when value='h5' />
             <when value='homer' />
             <when value='ginteractions' />
+            <when value='hicpro' />
         </conditional>
     </xml>
     <token name="@REFERENCES@">