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changeset 0:7f3d9a1a0447 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:37:07 -0500
parents
children 0c76d029dbe3
files mahotas_features.xml test-data/features.tsv test-data/galaxyIcon_noText.png
diffstat 3 files changed, 58 insertions(+), 0 deletions(-) [+]
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--- /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>
--- /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
Binary file test-data/galaxyIcon_noText.png has changed