Mercurial > repos > imgteam > mahotas_features

changeset 1:3aaf74f7515a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
author imgteam
date Wed, 17 Dec 2025 11:22:36 +0000
parents de5c698b251c
children
files mahotas_features.xml
diffstat 1 files changed, 28 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- a/mahotas_features.xml	Sat Feb 09 14:18:53 2019 -0500
+++ b/mahotas_features.xml	Wed Dec 17 11:22:36 2025 +0000
@@ -1,26 +1,35 @@
-<tool id="ip_mahotas_features" name="Mahotas-features" version="0.7">
-    <description>Compute features using mahotas</description>
+<tool id="ip_mahotas_features" name="Compute image features" version="0.7-2">
+    <description>with Mahotas</description>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="biii">mahotas-feature-computation</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="1.4.3">mahotas</requirement>
         <requirement type="package" version="4.0.0">pillow</requirement>
         <requirement type="package" version="1.12">numpy</requirement>
+        <requirement type="package" version="0.15.1">tifffile</requirement>
     </requirements>
-    <command detect_errors="aggressive"><![CDATA[mahotas-features.py
-#set files = '" "'.join( [ str( $file ) for $file in $inputs ] )
-"${files}"
+    <command detect_errors="aggressive"><![CDATA[
+        /usr/local/bin/mahotas-features.py
+        #set files = '" "'.join( [ str( $file ) for $file in $inputs ] )
+        "${files}"
 
---output $output
---convert-to-bw $convertbw
-$haralick 
-$lbp 
---clobber
-#if $lbpradius and $lbpradius is not None:
---lbp-radius $lbpradius
-#end if
+        --output $output
+        --convert-to-bw $convertbw
+        $haralick 
+        $lbp 
+        --clobber
+        #if $lbpradius and $lbpradius is not None:
+        --lbp-radius $lbpradius
+        #end if
 
-#if $lbppoints and $lbppoints is not None:
---lbp-points $lbppoints
-#end if]]></command>
+        #if $lbppoints and $lbppoints is not None:
+        --lbp-points $lbppoints
+        #end if]]>
+    </command>
     <inputs>
         <param name="inputs" type="data" format="tiff,png,jpg,bmp" multiple="True" label="Image files"/>
         <param name="convertbw" type="select" label="Convert color images to greyscale">
@@ -39,9 +48,9 @@
     <tests>
         <test>
             <param name="inputs" value="galaxyIcon_noText.png"/>
-            <param name="haralick" value="--haralick" />
-            <param name="lbp" value="--lbp" />
-            <param name="convertbw" value="max" />
+            <param name="haralick" value="true"/>
+            <param name="lbp" value="true"/>
+            <param name="convertbw" value="max"/>
             <output name="output" file="features.tsv" ftype="tsv" lines_diff="2"/>
         </test>
     </tests>