Fix weekly linting issues and tests

tools/2d_feature_extraction/2d_feature_extraction.xml

@@ -6,7 +6,7 @@
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <creator>
-        <expand macro="creators/bmcv" />
+        <expand macro="creators/bmcv"/>
     </creator>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
@@ -15,7 +15,7 @@
         <xref type="bio.tools">scikit-image</xref>
         <xref type="biii">scikit-image</xref>
     </xrefs>
-    <requirements> 
+    <requirements>
         <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
         <requirement type="package" version="2.2.2">pandas</requirement>
         <requirement type="package" version="1.23.3">numpy</requirement>
@@ -37,15 +37,15 @@
     ]]>
     </command>
     <inputs>
-        <param name="input_label" type="data" format="tiff,png" label="Label map" />
+        <param name="input_label" type="data" format="tiff,png" label="Label map"/>
         <conditional name="use_raw_option">
             <param label="Use the intensity image to compute additional features" name="use_raw" type="select">
                 <option selected="True" value="no_original">No intensity image</option>
                 <option value="raw_image">Use intensity image</option>
             </param>
-            <when value="no_original"></when>
+            <when value="no_original"/>
             <when value="raw_image">
-                <param name="input_raw" type="data" format="tiff,png" label="Intensity image" />
+                <param name="input_raw" type="data" format="tiff,png" label="Intensity image"/>
             </when>
         </conditional>
         <conditional name="feature_options">
@@ -84,13 +84,15 @@
         </conditional>
     </inputs>
     <outputs>
-       <data format="tabular" name="output" />
+        <data format="tabular" name="output"/>
     </outputs>
     <tests>
         <test>
-            <param name="input_label" value="input.tiff"/>
-            <param name="features" value="select"/>
-            <param name="selected_features" value="--label,--area"/>
+            <param name="input_label" value="input.tiff" ftype="tiff"/>
+            <conditional name="feature_options">
+                <param name="features" value="select"/>
+                <param name="selected_features" value="--label,--area"/>
+            </conditional>
             <output name="output" ftype="tabular" value="out.tsv"/>
         </test>
     </tests>

tools/2d_simple_filter/filter.xml

@@ -7,7 +7,7 @@
         <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <creator>
-        <expand macro="creators/bmcv" />
+        <expand macro="creators/bmcv"/>
     </creator>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
@@ -34,7 +34,7 @@
 
     ]]></command>
     <inputs>
-        <param name="input" type="data" format="tiff,png" label="Input image" />
+        <param name="input" type="data" format="tiff,png" label="Input image"/>
         <conditional name="filter">
             <param name="filter_type" type="select" label="Filter type">
                 <option value="gaussian" selected="True">Gaussian</option>
@@ -45,33 +45,35 @@
                 <option value="sobel_v">Sobel vertical</option>
             </param>
             <when value="gaussian">
-                <param name="size" type="float" value="3" min="0.1" label="Sigma" help="The half width of the Gaussian bell (in pixels)." />
+                <param name="size" type="float" value="3" min="0.1" label="Sigma" help="The half width of the Gaussian bell (in pixels)."/>
             </when>
             <when value="median">
-                <param name="size" type="integer" value="3" label="Radius" help="Radius of the neighborhood (in pixels)." />
+                <param name="size" type="integer" value="3" label="Radius" help="Radius of the neighborhood (in pixels)."/>
             </when>
             <when value="prewitt_h">
-                <param name="size" type="hidden" value="0" />
+                <param name="size" type="hidden" value="0"/>
             </when>
             <when value="prewitt_v">
-                <param name="size" type="hidden" value="0" />
+                <param name="size" type="hidden" value="0"/>
             </when>
             <when value="sobel_h">
-                <param name="size" type="hidden" value="0" />
+                <param name="size" type="hidden" value="0"/>
             </when>
             <when value="sobel_v">
-                <param name="size" type="hidden" value="0" />
+                <param name="size" type="hidden" value="0"/>
             </when>
         </conditional>
     </inputs>
     <outputs>
-       <data format="tiff" name="output" />
+        <data format="tiff" name="output"/>
     </outputs>
     <tests>
         <!-- Tests with uint8 TIFF input image -->
         <test>
-            <param name="input" value="input1_uint8.tiff" />
-            <param name="filter_type" value="gaussian" />
+            <param name="input" value="input1_uint8.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="gaussian"/>
+            </conditional>
             <expand macro="tests/intensity_image_diff" name="output" value="input1_gaussian.tiff" ftype="tiff">
                 <!--
 
@@ -88,37 +90,49 @@
             </expand>
         </test>
         <test>
-            <param name="input" value="input1_uint8.tiff" />
-            <param name="filter_type" value="median" />
+            <param name="input" value="input1_uint8.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="median"/>
+            </conditional>
             <expand macro="tests/intensity_image_diff" name="output" value="input1_median.tiff" ftype="tiff">
                 <!-- See note for Gaussian filter above. -->
                 <has_image_mean_intensity mean_intensity="63.67" eps="10"/>
             </expand>
         </test>
         <test>
-            <param name="input" value="input1_uint8.tiff" />
-            <param name="filter_type" value="prewitt_h" />
+            <param name="input" value="input1_uint8.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="prewitt_h"/>
+            </conditional>
             <expand macro="tests/intensity_image_diff" name="output" value="input1_prewitt_h.tiff" ftype="tiff"/>
         </test>
         <test>
-            <param name="input" value="input1_uint8.tiff" />
-            <param name="filter_type" value="prewitt_v" />
+            <param name="input" value="input1_uint8.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="prewitt_v"/>
+            </conditional>
             <expand macro="tests/intensity_image_diff" name="output" value="input1_prewitt_v.tiff" ftype="tiff"/>
         </test>
         <test>
-            <param name="input" value="input1_uint8.tiff" />
-            <param name="filter_type" value="sobel_h" />
+            <param name="input" value="input1_uint8.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="sobel_h"/>
+            </conditional>
             <expand macro="tests/intensity_image_diff" name="output" value="input1_sobel_h.tiff" ftype="tiff"/>
         </test>
         <test>
-            <param name="input" value="input1_uint8.tiff" />
-            <param name="filter_type" value="sobel_v" />
+            <param name="input" value="input1_uint8.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="sobel_v"/>
+            </conditional>
             <expand macro="tests/intensity_image_diff" name="output" value="input1_sobel_v.tiff" ftype="tiff"/>
         </test>
         <!-- Tests with float TIFF input image -->
         <test>
-            <param name="input" value="input2_float.tiff" />
-            <param name="filter_type" value="gaussian" />
+            <param name="input" value="input2_float.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="gaussian"/>
+            </conditional>
             <expand macro="tests/intensity_image_diff" name="output" value="input2_gaussian.tiff" ftype="tiff">
                 <!-- See note for Gaussian filter above. -->
                 <has_image_mean_intensity mean_intensity="0.25" eps="0.01"/>
@@ -133,6 +147,6 @@
 
     </help>
     <citations>
-       <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
+        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
     </citations>
 </tool>

tools/landmark_registration/landmark_registration.xml

@@ -1,5 +1,5 @@
 <tool id="ip_landmark_registration" name="Perform affine image registration (landmark-based)" version="0.1.0-2" profile="20.05">
-    <description></description>
+    <description/>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
     </edam_operations>
@@ -27,47 +27,53 @@
     ]]>
     </command>
     <inputs>
-        <param name="fn_lmkmov" type="data" format="tabular" label="Coordinates of moving landmarks (tsv file)" />
-        <param name="fn_lmkfix" type="data" format="tabular" label="Coordinates of fixed landmarks (tsv file)" />
+        <param name="fn_lmkmov" type="data" format="tabular" label="Coordinates of moving landmarks (tsv file)"/>
+        <param name="fn_lmkfix" type="data" format="tabular" label="Coordinates of fixed landmarks (tsv file)"/>
         <conditional name="algo_option">
             <param name="algo" type="select" label="Select the algorithm">
                 <option value="ransac">Affine Transformation (based on RANSAC)</option>
                 <option value="ls">Affine Transformation (based on Least Squares)</option>
                 <option value="pwat" selected="True">Piecewise Affine Transformation</option>
             </param>
             <when value="ransac">
-                <param name="res_th" type="float" value="2.0" label="Maximum distance for a data point to be classified as an inlier." />
-                <param name="max_ite" type="integer" value="100" label="Maximum number of iterations for random sample selection." />
+                <param name="res_th" type="float" value="2.0" label="Maximum distance for a data point to be classified as an inlier."/>
+                <param name="max_ite" type="integer" value="100" label="Maximum number of iterations for random sample selection."/>
             </when>
-            <when value="ls"></when>
+            <when value="ls"/>
             <when value="pwat">
-                <param name="fn_ptsmov" type="data" format="tabular" label="Coordinates of points to be transformed (tsv file)" />
+                <param name="fn_ptsmov" type="data" format="tabular" label="Coordinates of points to be transformed (tsv file)"/>
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format="tabular" name="fn_out" />
+        <data format="tabular" name="fn_out"/>
     </outputs>
     <tests>
         <test>
             <param name="fn_lmkmov" value="points_moving.tsv"/>
             <param name="fn_lmkfix" value="points_fixed.tsv"/>
-            <param name="algo" value="ls"/>
+            <conditional name="algo_option">
+                <param name="algo" value="ls"/>
+            </conditional>
             <output name="fn_out" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
         </test>
         <test>
             <param name="fn_lmkmov" value="points_moving.tsv"/>
             <param name="fn_lmkfix" value="points_fixed.tsv"/>
-            <param name="algo" value="ransac"/>
-            <param name="res_th" value="2.0"/>
-            <param name="max_ite" value="100"/>
+            <conditional name="algo_option">
+                <param name="algo" value="ransac"/>
+                <param name="res_th" value="2.0"/>
+                <param name="max_ite" value="100"/>
+            </conditional>
             <output name="fn_out" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
         </test>
         <test>
             <param name="fn_lmkmov" value="lmk_mov.tsv"/>
             <param name="fn_lmkfix" value="lmk_fix.tsv"/>
-            <param name="algo" value="pwat"/>
-            <param name="fn_ptsmov" value="points.tsv"/>
+            <conditional name="algo_option">
+                <param name="algo" value="pwat"/>
+                <param name="fn_ptsmov" value="points.tsv"/>
+            </conditional>
             <output name="fn_out" value="points_pwlt.tsv" ftype="tabular"/>
         </test>
     </tests>

tools/mahotas_features/mahotas_features.xml

@@ -11,23 +11,25 @@
         <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}"
+    </requirements>
+    <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">
@@ -46,9 +48,9 @@ $lbp
     <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>