Mercurial > repos > thomaswollmann > mahotas_features

changeset 1:a95f9d6ea1ca draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit 6dd3802614ab7940792e184944fc90d78c71cf51
author thomaswollmann
date Tue, 03 Jan 2017 04:36:24 -0500
parents f2ed647d792c
children
files mahotas_features.xml test-data/features.tsv test-data/galaxyIcon_noText.png
diffstat 3 files changed, 35 insertions(+), 37 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features.tsv	Tue Jan 03 04:36:24 2017 -0500
@@ -0,0 +1,2 @@
+	mean:Angular Second Moment	mean:Contrast	mean:Correlation	mean:Sum of Squares: Variance	mean:Inverse Difference Moment	mean:Sum Average	mean:Sum Variance	mean:Sum Entropy	mean:Entropy	mean:Difference Variance	mean:Difference Entropy	mean:Information Measure of Correlation 1	mean:Information Measure of Correlation 2	ptp:Angular Second Moment	ptp:Contrast	ptp:Correlation	ptp:Sum of Squares: Variance	ptp:Inverse Difference Moment	ptp:Sum Average	ptp:Sum Variance	ptp:Sum Entropy	ptp:Entropy	ptp:Difference Variance	ptp:Difference Entropy	ptp:Information Measure of Correlation 1	ptp:Information Measure of Correlation 2	lbp_r8_p6_0	lbp_r8_p6_1	lbp_r8_p6_2	lbp_r8_p6_3	lbp_r8_p6_4	lbp_r8_p6_5	lbp_r8_p6_6	lbp_r8_p6_7	lbp_r8_p6_8	lbp_r8_p6_9	lbp_r8_p6_10	lbp_r8_p6_11	lbp_r8_p6_12	lbp_r8_p6_13
+galaxyIcon_noText.png	0.282375896829	5971.829075	0.716963415834	10558.0340615	0.807748866113	372.165112179	36260.3071712	2.52066662394	2.73555338992	0.00252122763136	1.36304068933	-0.552303235256	0.932070076794	0.0388473044444	3822.8812	0.181903435512	331.650449629	0.122129460944	4.75788461538	3935.03677629	0.318315119007	0.437719347337	0.000763750451389	0.683142134762	0.226647260141	0.0547750277851	386.0	79.0	106.0	5.0	47.0	0.0	0.0	0.0	27.0	0.0	0.0	0.0	0.0	0.0
Binary file test-data/galaxyIcon_noText.png has changed