# HG changeset patch
# User imgteam
# Date 1549741027 18000
# Node ID 7f3d9a1a044762d1a8288152c298c4603a61188c

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581

diff -r 000000000000 -r 7f3d9a1a0447 mahotas_features.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mahotas_features.xml	Sat Feb 09 14:37:07 2019 -0500
@@ -0,0 +1,56 @@
+<tool id="ip_mahotas_features" name="Mahotas-features" version="0.7">
+    <description>Compute features using mahotas</description>
+    <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>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[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
+
+#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">
+            <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="tsv" hidden="false" name="output"/>
+    </outputs>
+    <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>
+    **What it does**
+
+    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>
+</tool>
diff -r 000000000000 -r 7f3d9a1a0447 test-data/features.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features.tsv	Sat Feb 09 14:37:07 2019 -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
diff -r 000000000000 -r 7f3d9a1a0447 test-data/galaxyIcon_noText.png
Binary file test-data/galaxyIcon_noText.png has changed