diff ashlar.xml @ 4:0b8423c7ee3e draft default tip

planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit d1f9d43d20432cc958e340271ba63c85a17ff338

--- a/ashlar.xml	Fri Feb 09 22:48:46 2024 +0000
+++ b/ashlar.xml	Wed Feb 26 18:09:34 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="ashlar" name="ASHLAR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
+<tool id="ashlar" name="ASHLAR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
     <description>Alignment by Simultaneous Harmonization of Layer/Adjacency Registration</description>
     <macros>
         <import>macros.xml</import>
@@ -81,6 +81,12 @@
         $adv.flip_mosaic_y
 
         -o registered.ome.tif;
+
+        #if $rename.decide == "do_rename"
+            python3 '${__tool_directory__}/rename_channels.py'
+            --image registered.ome.tif
+            --markers '$rename.markers_file';
+        #end if
     ]]></command>
 
     <inputs>
@@ -90,6 +96,17 @@
         <param name="flip_x" type="boolean" truevalue="--flip-x" falsevalue="" label="Flip X-axis"/>
         <param name="flip_y" type="boolean" truevalue="--flip-y" falsevalue="" label="Flip Y-axis"/>
         <param name="max_shift" type="integer" value="30" label="Maximum allowed per-tile corrective shift" help="In micros"/>
+        <conditional name="rename">
+            <param name="decide" type="select" label="Rename channels in OME-XML metadata">
+                <option value="do_rename">Rename channels</option>
+                <option value="dont_rename" selected="true">Leave channel indices</option>
+            </param>
+            <when value="do_rename">
+                <param name="markers_file" type="data" format="csv" label="Markers File"/>
+            </when>
+            <when value="dont_rename">
+            </when>
+        </conditional>
         <section name="adv" title="Advanced Options" expanded="false">
             <param name="align_channel" type="integer" value="0" label="Align Channel Number"/>
             <param name="stitch_alpha" type="float" optional="true" label="Alpha"/>
@@ -117,6 +134,28 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="lraw">
+                <collection type="list">
+                    <element name="rR1" value="ashlar_test_c0.tiff" />
+                    <element name="rR2" value="ashlar_test_c1.tiff" />
+                </collection>
+            </param>
+            <conditional name="rename">
+                <param name="decide" value="do_rename" />
+                <param name="markers_file" value="ashlar_test_markers.csv" />
+            </conditional>
+            <output name="output" ftype="ome.tiff">
+                <assert_contents>
+                    <has_size value="500000" delta="400000" />
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text text="DAPI" />
+                <has_text text="CD3" />
+                <has_text text="µm" />
+            </assert_stdout>
+        </test>
     </tests>
     <help><![CDATA[
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