diff mahotas_features.xml @ 1:a95f9d6ea1ca draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit 6dd3802614ab7940792e184944fc90d78c71cf51

--- a/mahotas_features.xml	Sat Dec 31 09:12:04 2016 -0500
+++ b/mahotas_features.xml	Tue Jan 03 04:36:24 2017 -0500
@@ -1,58 +1,54 @@
-<tool id="mahotas_features" name="mahotas-features" version="0.1">
+<tool id="mahotas_features" name="mahotas-features" version="0.6">
   <requirements>
-    <requirement type="package" version="1.4.3">mahotas</requirement>
     <requirement type="package">mahotas</requirement>
+    <requirement type="package">pillow</requirement>
     <requirement type="package">numpy</requirement>
   </requirements>
   <description>Compute features using mahotas</description>
   <stdio>
     <exit_code level="fatal" range="1:"/>
   </stdio>
-  <version_command>python mahotas-features.py --version</version_command>
-  <command interpreter="python"><![CDATA[mahotas-features.py 
-#set repeat_var_1 = '" "'.join([ str($var.positional_1) for $var in $repeat_1 ])
-"$repeat_var_1"
+  <command><![CDATA[mahotas-features.py
+#set files = '" "'.join( [ str( $file ) for $file in $inputs ] )
+"${files}"
 
-
-#if $output and $output is not None:
 --output $output
-#end if
-$clobber
-
-#if $convert-to-bw and $convert-to-bw is not None:
---convert-to-bw $convert-to-bw
-#end if
-$no-color
-$haralick
-$lbp
-
-#if $lbp-radius and $lbp-radius is not None:
---lbp-radius $lbp-radius
+--convert-to-bw $convertbw
+$haralick 
+$lbp 
+--clobber
+#if $lbpradius and $lbpradius is not None:
+--lbp-radius $lbpradius
 #end if
 
-#if $lbp-points and $lbp-points is not None:
---lbp-points $lbp-points
-#end if
-> $default]]></command>
+#if $lbppoints and $lbppoints is not None:
+--lbp-points $lbppoints
+#end if]]></command>
   <inputs>
-    <repeat min="1" name="repeat_1" title="repeat_title">
-      <param area="false" label="Image files names" name="positional_1" type="text"/>
-    </repeat>
-    <param area="false" help="(--output)" label="Output file for feature files" name="output" optional="true" type="text" value="features.tsv"/>
-    <param checked="false" help="(--clobber)" label="Overwrite output file (if it exists)" name="clobber" type="boolean" truevalue="--clobber" falsevalue=""/>
-    <param area="false" help="(--convert-to-bw)" label="Convert color images to greyscale.&#10;Acceptable values:&#10;&#9;no: raises an error (default)&#10;&#9;max: use max projection&#10;&#9;yes: use rgb2gray" name="convert-to-bw" optional="true" type="text" value="no"/>
-    <param checked="false" help="(--no-color)" label="Do not print in color (for error and warning messages)" name="no-color" type="boolean" truevalue="--no-color" falsevalue=""/>
-    <param checked="false" help="(--haralick)" label="Compute Haralick features" name="haralick" type="boolean" truevalue="--haralick" falsevalue=""/>
-    <param checked="false" help="(--lbp)" label="Compute LBP (linear binary patterns) features" name="lbp" type="boolean" truevalue="--lbp" falsevalue=""/>
-    <param help="(--lbp-radius)" label="Radius to use for LBP features" name="lbp-radius" optional="true" type="integer" value="8"/>
-    <param help="(--lbp-points)" label="Nr of points to use for LBP features" name="lbp-points" optional="true" type="integer" value="6"/>
+    <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">
+        <option value="no" selected="True">no</option>
+        <option value="max">max projection</option>
+        <option value="yes">yes</option>
+    </param>
+    <param checked="true" help="(--haralick)" label="Compute Haralick features" name="haralick" type="boolean" truevalue="--haralick" falsevalue=""/>
+    <param checked="true" help="(--lbp)" label="Compute LBP (linear binary patterns) features" name="lbp" type="boolean" truevalue="--lbp" falsevalue=""/>
+    <param help="(--lbp-radius)" label="Radius to use for LBP features" name="lbpradius" optional="true" type="integer" value="8"/>
+    <param help="(--lbp-points)" label="Nr of points to use for LBP features" name="lbppoints" optional="true" type="integer" value="6"/>
   </inputs>
   <outputs>
-    <data format="txt" hidden="false" name="default"/>
+    <data format="tsv" hidden="false" name="output"/>
   </outputs>
-  <help>Compute features using mahotas</help>
   <tests>
+    <test>
+	    <param name="inputs" value="galaxyIcon_noText.png"/>
+	    <param name="haralick" value="--haralick" />
+	    <param name="lbp" value="--lbp" />
+	    <param name="convertbw" value="max" />
+	    <output name="output" file="features.tsv" ftype="tsv" lines_diff="2"/>
+    </test>
   </tests>
+  <help>Mahotas is a computer vision and image processing library for Python. This tools computes features using mahotas.</help>
   <citations>
       <citation type="doi">10.5334/jors.ac</citation>
   </citations>