New version of pretextmap and addition of --highres flag (#7721)

* new version of pretextmap and add highres flag

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

* Update tools/pretext/pretext_map.xml

---------

Co-authored-by: Claude <noreply@anthropic.com>
Co-authored-by: Saim Momin <64724322+SaimMomin12@users.noreply.github.com>

Author: 3 people

tools/pretext/pretext_map.xml

@@ -1,8 +1,8 @@
 <tool id="pretext_map" name="PretextMap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>converts SAM or BAM files into genome contact maps</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.1.9</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@TOOL_VERSION@">0.2.3</token>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">pretextmap</requirement>
@@ -31,10 +31,12 @@
         #elif $filter.filter_type == "out":
             --filterExclude '$filter.filter_list'
         #end if 
+        $highRes
         -o output.pretext
     ]]></command>
     <inputs>
         <param name="input" type="data" format="sam,bam" label="Input dataset in SAM or BAM format"/>
+        <param argument="--highRes" type="boolean" truevalue="--highRes" falsevalue="" label="High resolution mode" help="Use high resolution mode for better contact map resolution"/>
         <conditional name="sorting">
             <param argument="--sortby" type="select" label="Sort by" help="Sort the genome by length or name of the scaffolds">
                 <option value="nosort">Don't sort</option>
@@ -91,6 +93,7 @@
     <tests>
         <test>
             <param name="input" ftype="bam" value="test.bam"/>
+            <param name="highRes" value="true"/>
             <conditional name="sorting">
                 <param name="sortby" value="length"/>
                 <param name="sortorder" value="ascend"/>
@@ -100,10 +103,15 @@
                 <param name="filter_list" value="ref"/>
             </conditional>
             <param name="map_qual" value="10"/>
-            <output name="pretext_map_out" file="output_1.pretext"/>
+            <output name="pretext_map_out">
+                <assert_contents>
+                    <has_size value="2225023" delta="1000"/>
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="input" ftype="sam" value="test.sam"/>
+            <param name="highRes" value="false"/>
             <conditional name="sorting">
                 <param name="sortby" value="name"/>
                 <param name="sortorder" value="descend"/>