imagej2_noise: imagej2_noise.xml comparison

comparison imagej2_noise.xml @ 1:7a44772cc89f draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"

author	imgteam
date	Mon, 28 Sep 2020 16:45:49 +0000
parents	3f6599ec7d30
children	756e062741dc

comparison

equal deleted inserted replaced

-:3f6599ec7d30
+:7a44772cc89f
-<?xml version='1.0' encoding='UTF-8'?>
 <tool id="imagej2_noise" name="Add or remove noise" version="@WRAPPER_VERSION@.0">
 <description></description>
 <macros>
 <import>imagej2_macros.xml</import>
 <xml name="insertion_select">
 <option value="additive" selected="True">Additive</option>
 <option value="multiplicative">Multiplicative</option>
 </param>
 </xml>
 </macros>
-<expand macro="fiji_requirements" />
+<expand macro="fiji_requirements"/>
-<command>
+<command detect_errors="exit_code"><![CDATA[
-<![CDATA[
+#import os
-python $__tool_directory__/imagej2_noise.py
+#set error_log = 'output_log.txt'
---input "$input"
+#if str($noise_cond.noise) == 'randomj':
---input_datatype $input.ext
+#set randomj_value = $noise_cond.randomj_cond.randomj
---noise $noise_cond.noise
+#else:
-#if $noise_cond.noise == 'add_specified_noise':
+#set randomj_value = None
---standard_deviation $noise_cond.standard_deviation
+#end if
-#else if $noise_cond.noise == 'remove_outliers':
+#set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
---radius $noise_cond.radius
+#set input_with_ext = '.'.join([input_sans_ext, $input.ext])
---threshold $noise_cond.threshold
+ln -s '$input.file_name' '$input_with_ext' &&
---which_outliers $noise_cond.which_outliers
+#set output_filename = '.'.join(['output', $input.ext])
-#else if $noise_cond.noise == 'randomj':
+touch '$output_filename' &&
---randomj $noise_cond.randomj_cond.randomj
+touch '$error_log' &&
-#if $noise_cond.randomj_cond.randomj == 'randomj_binomial':
+ImageJ --ij2 --headless --debug
---trials $noise_cond.randomj_cond.trials
+--jython '$__tool_directory__/imagej2_noise_jython_script.py'
---probability $noise_cond.randomj_cond.probability
+'$error_log'
-#else if $noise_cond.randomj_cond.randomj == 'randomj_exponential':
+'$input_with_ext'
---lammbda $noise_cond.randomj_cond.lammbda
+'$input.ext'
-#else if $noise_cond.randomj_cond.randomj == 'randomj_gamma':
+'$noise_cond.noise'
---order $noise_cond.randomj_cond.order
+#if $noise_cond.noise == 'add_specified_noise':
-#else if $noise_cond.randomj_cond.randomj == 'randomj_gaussian':
+$noise_cond.standard_deviation
---mean $noise_cond.randomj_cond.mean
+#else:
---sigma $noise_cond.randomj_cond.sigma
+'None'
-#else if $noise_cond.randomj_cond.randomj == 'randomj_poisson':
+#end if
---mean $noise_cond.randomj_cond.mean
+#if $noise_cond.noise == 'remove_outliers':
-#else if $noise_cond.randomj_cond.randomj == 'randomj_uniform':
+$noise_cond.radius
---min $noise_cond.randomj_cond.min
+$noise_cond.threshold
---max $noise_cond.randomj_cond.max
+'$noise_cond.which_outliers'
-#end if
+#else:
---insertion $noise_cond.randomj_cond.insertion
+'None'
+'None'
+'None'
+#end if
+'$randomj_value'
+#if $randomj_value == 'randomj_binomial':
+$noise_cond.randomj_cond.trials
+$noise_cond.randomj_cond.probability
+#else:
+'None'
+'None'
+#end if
+#if $randomj_value == 'randomj_exponential':
+$noise_cond.randomj_cond.lammbda
+#else:
+'None'
+#end if
+#if $randomj_value == 'randomj_gamma':
+$noise_cond.randomj_cond.order
+#else:
+'None'
+#end if
+#if $randomj_value in['randomj_gaussian', 'randomj_poisson']:
+$noise_cond.randomj_cond.mean
+#if $randomj_value == 'randomj_gaussian':
+$noise_cond.randomj_cond.sigma
+#else:
+'None'
 #end if
---jython_script $__tool_directory__/imagej2_noise_jython_script.py
+#else:
---output "$output"
+'None'
-]]>
+'None'
-</command>
+#end if
+#if $randomj_value == 'randomj_uniform':
+$noise_cond.randomj_cond.min
+$noise_cond.randomj_cond.max
+#else:
+'None'
+'None'
+#end if
+#if str($randomj_value) != 'None':
+'$noise_cond.randomj_cond.insertion'
+#else:
+'None'
+#end if
+'$output_filename'
+&>'$error_log';
+if [[ $? -ne 0 ]]; then
+cat '$error_log' >&2;
+else
+mv '$output_filename' '$output';
+fi
+]]></command>
 <inputs>
-<param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
+<expand macro="param_input"/>
 <conditional name="noise_cond">
 <param name="noise" type="select" label="Noise">
 <option value="add_noise" selected="True">Add Random Noise</option>
 <option value="add_specified_noise">Add Specified Noise</option>
 <option value="salt_and_pepper">Salt and Pepper</option>
 <option value="remove_outliers">Remove Outliers</option>
 <option value="remove_nans">Remove NaNs</option>
 <option value="rof_denoise">ROF Denoise</option>
 <option value="randomj">RandomJ</option>
 </param>
-<when value="add_noise" />
+<when value="add_noise"/>
 <when value="add_specified_noise">
 <param name="standard_deviation" type="float" value="25.0" label="Standard deviation" help="Floating point number"/>
 </when>
-<when value="salt_and_pepper" />
+<when value="salt_and_pepper"/>
-<when value="despeckle" />
+<when value="despeckle"/>
 <when value="remove_outliers">
 <param name="radius" type="float" value="2.0" label="Radius" help="pixels"/>
 <param name="threshold" type="float" value="50.0" label="Threshold"/>
 <param name="which_outliers" type="select" label="Which Outliers">
 <option value="bright" selected="True">Bright</option>
 <option value="dark">Dark</option>
 </param>
 </when>
-<when value="remove_nans" />
+<when value="remove_nans"/>
-<when value="rof_denoise" />
+<when value="rof_denoise"/>
 <when value="randomj">
 <conditional name="randomj_cond">
 <param name="randomj" type="select" label="RandomJ">
 <option value="randomj_binomial" selected="True">RandomJ Binomial</option>
 <option value="randomj_exponential">RandomJ Exponential</option>
 <option value="randomj_uniform">RandomJ Uniform</option>
 </param>
 <when value="randomj_binomial">
 <param name="trials" type="float" value="1.0" label="Trials"/>
 <param name="probability" type="float" value="0.5" label="Probability"/>
-<expand macro="insertion_select" />
+<expand macro="insertion_select"/>
 </when>
 <when value="randomj_exponential">
 <param name="lammbda" type="float" value="0.5" label="Lambda"/>
-<expand macro="insertion_select" />
+<expand macro="insertion_select"/>
 </when>
 <when value="randomj_gamma">
 <param name="order" type="integer" value="1" label="Order"/>
-<expand macro="insertion_select" />
+<expand macro="insertion_select"/>
 </when>
 <when value="randomj_gaussian">
 <param name="mean" type="float" value="0.0" label="Mean"/>
 <param name="sigma" type="float" value="1.0" label="Sigma"/>
-<expand macro="insertion_select" />
+<expand macro="insertion_select"/>
 </when>
 <when value="randomj_poisson">
 <param name="mean" type="float" value="1.0" label="Mean"/>
-<expand macro="insertion_select" />
+<expand macro="insertion_select"/>
 </when>
 <when value="randomj_uniform">
 <param name="min" type="float" value="0.0" label="Min"/>
 <param name="max" type="float" value="1.0" label="Max"/>
-<expand macro="insertion_select" />
+<expand macro="insertion_select"/>
 </when>
 </conditional>
 </when>
 </conditional>
 </inputs>
 <outputs>
-<data name="output" format_source="input" label="${tool.name} on ${on_string}: ${noise_cond.noise.replace( '_', ' ' )}" />
+<data name="output" format_source="input"/>
 </outputs>
 <tests>
 <test>
-<param name="input" value="blobs.gif" />
+<param name="input" value="blobs.gif"/>
-<param name="input_datatype" value="gif" />
+<param name="noise" value="add_specified_noise"/>
-<param name="noise" value="add_specified_noise" />
+<output name="output" file="add_specified_noise.gif"/>
-<output name="output" file="add_specified_noise.gif" />
 </test>
 <test>
-<param name="input" value="blobs.gif" />
+<param name="input" value="blobs.gif"/>
-<param name="input_datatype" value="gif" />
+<param name="noise" value="despeckle"/>
-<param name="noise" value="despeckle" />
+<output name="output" file="despeckle.gif"/>
-<output name="output" file="despeckle.gif" />
 </test>
 <test>
-<param name="input" value="blobs.gif" />
+<param name="input" value="blobs.gif"/>
-<param name="input_datatype" value="gif" />
+<param name="noise" value="remove_outliers"/>
-<param name="noise" value="remove_outliers" />
+<output name="output" file="remove_outliers.gif"/>
-<param name="radius" value="2.0" />
-<param name="threshold" value="50.0" />
-<param name="which_outliers" value="bright" />
-<output name="output" file="remove_outliers.gif" />
 </test>
 </tests>
 <help>
 **What it does**
 - **RandonJ Gaussian** - Contaminates image with random numbers generated using a Gaussian random variable.
 - **RandonJ Poisson** - Contaminates image with random numbers generated using a Poisson random variable.
 - **RandonJ Uniform** - Contaminates image with random numbers generated using a uniform random variable.
 ]]>
 </help>
-<expand macro="fiji_headless_citations" />
+<expand macro="fiji_headless_citations"/>
 </tool>

Mercurial > repos > imgteam > imagej2_noise

comparison imagej2_noise.xml @ 1:7a44772cc89f draft