Merge pull request #6663 from hugolefeuvre/update_groot

Update groot
galaxyproject · Jan 8, 2025 · 90b5334 · 90b5334
2 parents 772b364 + 8cfdea1
commit 90b5334
Showing 1 changed file with 23 additions and 13 deletions.
diff --git a/tools/groot/groot.xml b/tools/groot/groot.xml
@@ -2,7 +2,7 @@
     <description> align reads to references and weight variation graphs and generate report</description>
     <macros>
         <token name="@TOOL_VERSION@">1.1.2</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
         <token name="@PROFILE@">22.05</token>
     </macros>
     <xrefs>
@@ -35,8 +35,11 @@ groot align
     --processors "\${GALAXY_SLOTS:-1}"
 
 | groot report
+    #if str($coverage.mode) == "cutoff"
     --covCutoff '$covCutoff'
-    $lowCov
+    #elif str($coverage.mode) == "lowcov"
+    --lowCov
+    #end if
     > '$report_out'
 
 ]]></command>
@@ -58,13 +61,20 @@ groot align
         <section name="align" title="Align">
             <param argument="--contThresh" type="float" min="0" max="1.0" value="0.99" label="Containment threshold for the LSH ensemble" />
             <param argument="--minKmerCov" type="integer" min="0" value="1" label="Minimum number of k-mers covering each base of a graph segment" />
-            <param argument="--noAlign" type="boolean" truevalue="" falsevalue="--noAlign" label="Perform exact alignment?" 
-                help="If not, graphs will still be weighted using approximate read mappings"/>
+            <param argument="--noAlign" type="boolean" checked="true" truevalue="" falsevalue="--noAlign" label="Perform exact alignment?" 
+                help="If 'No', --noAlign will be set, no exact alignment will be performed and graphs will still be weighted using approximate read mappings"/>
         </section>
         <section name="report" title="Report">
-            <param argument="--covCutoff" type="float" min="0" max="1.0" value="0.97" label="Coverage cutoff for reporting ARGs" />
-            <param argument="--lowCov" type="boolean" checked="false" truevalue="--lowCov" falsevalue="" label="Report ARGs which may not be covered at the 5'/3' ends" 
-                help="If 'Yes', overrides --covCutoff option"/>
+            <conditional name="coverage">
+                <param name="mode" type="select" label="Choose your coverage mode" help="" >
+                    <option value="cutoff" selected="true">Choose your coverage cutoff</option>
+                    <option value="lowcov">Low coverage (will report ARGs which may not be covered at the 5’/3’ ends)</option>
+                </param>
+                <when value="cutoff">
+                    <param argument="--covCutoff" type="float" min="0" max="1.0" value="0.97" label="Coverage cutoff for reporting ARGs" />
+                </when>
+                <when value="lowcov"/>
+            </conditional>
         </section>
     </inputs>
     <outputs>
@@ -85,11 +95,10 @@ groot align
             <section name="align">
                 <param name="contThresh" value="0.99"/>
                 <param name="minKmerCov" value="1" />
-                <param name="noAlign" value=""/>
             </section>
             <section name="report">
-                <conditional name="arg_report">
-                    <param name="criteria" value="cutoff" />
+                <conditional name="coverage">
+                    <param name="mode" value="cutoff"/>
                     <param name="covCutoff" value="0.97" />
                 </conditional>
             </section>
@@ -115,11 +124,12 @@ groot align
             <section name="align">
                 <param name="contThresh" value="0.99"/>
                 <param name="minKmerCov" value="1" />
-                <param name="noAlign" value=""/>
+                <param name="noAlign" value="true"/>
             </section>
             <section name="report">
-                <param name="covCutoff" value="0.97" />
-                <param name="lowCov" value="True"/>
+                <conditional name="coverage">
+                    <param name="mode" value="lowcov"/>
+                </conditional>
             </section>
             <output name="report_out" ftype="tabular">
                 <assert_contents>