Mercurial > repos > imgteam > imagej2_find_maxima
comparison imagej2_find_maxima.xml @ 1:e2622ebb5ce4 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author | imgteam |
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date | Mon, 28 Sep 2020 16:49:43 +0000 |
parents | 29b39f5b0e69 |
children | 6a07f71806bb |
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0:29b39f5b0e69 | 1:e2622ebb5ce4 |
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1 <?xml version='1.0' encoding='UTF-8'?> | 1 <tool id="imagej2_find_maxima" name="Find maxima" version="@WRAPPER_VERSION@.1"> |
2 <tool id="imagej2_find_maxima" name="Find maxima" version="@WRAPPER_VERSION@.0"> | |
3 <description></description> | 2 <description></description> |
4 <macros> | 3 <macros> |
5 <import>imagej2_macros.xml</import> | 4 <import>imagej2_macros.xml</import> |
6 </macros> | 5 </macros> |
7 <expand macro="fiji_requirements" /> | 6 <expand macro="fiji_requirements"/> |
8 <command> | 7 <command detect_errors="exit_code"><![CDATA[ |
9 <![CDATA[ | 8 #import os |
10 python $__tool_directory__/imagej2_find_maxima.py | 9 #set error_log = 'output_log.txt' |
11 --input "$input" | 10 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0] |
12 --input_datatype $input.ext | 11 #set input_with_ext = '.'.join([input_sans_ext, $input.ext]) |
13 --scale_when_converting $scale_when_converting | 12 ln -s '$input.file_name' '$input_with_ext' && |
14 --weighted_rgb_conversions $weighted_rgb_conversions | 13 #if str($output_type) == 'List' or str($output_type) == 'Count': |
15 --noise_tolerance $noise_tolerance | 14 #set list_or_count = True |
16 --output_type $output_type | 15 #else: |
17 --exclude_edge_maxima $exclude_edge_maxima | 16 #set output_filename = '.'.join(['output', $input.ext]) |
18 --light_background $light_background | 17 touch '$output_filename' && |
19 --jython_script $__tool_directory__/imagej2_find_maxima_jython_script.py | 18 #set list_or_count = False |
20 #if str( $output_type ) == "List" or str( $output_type ) == "Count": | 19 #end if |
21 --output "$results" | 20 touch '$error_log' && |
22 --output_datatype "tabular" | 21 ImageJ --ij2 --headless --debug |
22 --jython '$__tool_directory__/imagej2_find_maxima_jython_script.py' | |
23 '$error_log' | |
24 '$input_with_ext' | |
25 '$scale_when_converting' | |
26 '$weighted_rgb_conversions' | |
27 $noise_tolerance | |
28 '$output_type' | |
29 '$exclude_edge_maxima' | |
30 '$light_background' | |
31 #if $list_or_count: | |
32 '$results' | |
33 'tabular' | |
34 #else: | |
35 '$output_filename' | |
36 '$input.ext' | |
37 #end if | |
38 &>'$error_log'; | |
39 if [[ $? -ne 0 ]]; then | |
40 cat '$error_log' >&2; | |
41 else | |
42 #if $list_or_count: | |
43 mv '$results' '$output'; | |
23 #else: | 44 #else: |
24 --output "$output" | 45 mv '$output_filename' '$output'; |
25 --output_datatype $output.ext | |
26 #end if | 46 #end if |
27 ]]> | 47 fi |
28 </command> | 48 ]]></command> |
29 <inputs> | 49 <inputs> |
30 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/> | 50 <expand macro="param_input"/> |
31 <param name="noise_tolerance" type="integer" value="10" min="0" label="Noise tolerance" help="Maxima are ignored if they do not stand out from the surroundings by more than this value."/> | 51 <param name="noise_tolerance" type="integer" value="10" min="0" label="Noise tolerance" help="Maxima are ignored if they do not stand out from the surroundings by more than this value."/> |
32 <param name="output_type" type="select" label="Output type"> | 52 <param name="output_type" type="select" label="Output type"> |
33 <option value="Single_Points" selected="True">Single Points</option> | 53 <option value="Single_Points" selected="True">Single Points</option> |
34 <option value="Maxima_Within_Tolerance">Maxima Within Tolerance</option> | 54 <option value="Maxima_Within_Tolerance">Maxima Within Tolerance</option> |
35 <option value="Segmented_Particles">Segmented Particles</option> | 55 <option value="Segmented_Particles">Segmented Particles</option> |
57 <option value="no" selected="True">No</option> | 77 <option value="no" selected="True">No</option> |
58 <option value="yes">Yes</option> | 78 <option value="yes">Yes</option> |
59 </param> | 79 </param> |
60 </inputs> | 80 </inputs> |
61 <outputs> | 81 <outputs> |
62 <data name="output" format_source="input" label="${tool.name} on ${on_string}: ${output_type}"> | 82 <data name="output" format_source="input"> |
63 <filter>output_type != "List" and output_type != "Count"</filter> | 83 <filter>output_type != "List" and output_type != "Count"</filter> |
64 </data> | 84 </data> |
65 <data name="results" format="tabular" label="${tool.name} on ${on_string}: ${output_type}"> | 85 <data name="results" format="tabular"> |
66 <filter>output_type == "List" or output_type == "Count"</filter> | 86 <filter>output_type == "List" or output_type == "Count"</filter> |
67 </data> | 87 </data> |
68 </outputs> | 88 </outputs> |
69 <tests> | 89 <tests> |
70 <test> | 90 <test> |
71 <param name="input" value="blobs.gif" /> | 91 <param name="input" value="blobs.gif"/> |
72 <output name="output" file="blobs_single_points.gif" compare="sim_size" /> | 92 <output name="output" file="blobs_single_points.gif" compare="sim_size"/> |
73 </test> | 93 </test> |
74 <test> | 94 <test> |
75 <param name="input" value="blobs.gif" /> | 95 <param name="input" value="blobs.gif"/> |
76 <param name="noise_tolerance" value="13" /> | 96 <param name="noise_tolerance" value="13"/> |
77 <param name="output_type" value="Maxima_Within_Tolerance" /> | 97 <param name="output_type" value="Maxima_Within_Tolerance"/> |
78 <output name="output" file="blobs_tolerance.gif" compare="sim_size" /> | 98 <output name="output" file="blobs_tolerance.gif" compare="sim_size"/> |
79 </test> | 99 </test> |
80 <test> | 100 <test> |
81 <param name="input" value="blobs.gif" /> | 101 <param name="input" value="blobs.gif"/> |
82 <param name="noise_tolerance" value="16" /> | 102 <param name="noise_tolerance" value="16"/> |
83 <param name="output_type" value="Segmented_Particles" /> | 103 <param name="output_type" value="Segmented_Particles"/> |
84 <param name="exclude_edge_maxima" value="yes" /> | 104 <param name="exclude_edge_maxima" value="yes"/> |
85 <output name="output" file="blobs_segmented.gif" compare="sim_size" /> | 105 <output name="output" file="blobs_segmented.gif" compare="sim_size"/> |
86 </test> | 106 </test> |
87 <!-- | 107 <!-- |
88 This version of Fiji does not produce the same resultsTable | 108 This version of Fiji does not produce the same resultsTable |
89 as the previous version, so eliminating these options until | 109 as the previous version, so eliminating these options until |
90 there is time to investigate | 110 there is time to investigate |
130 - **Exclude Edge Maxima** - Excludes maxima if the area within the noise tolerance surrounding a maximum touches the edge of the image (edge of the selection does not matter). | 150 - **Exclude Edge Maxima** - Excludes maxima if the area within the noise tolerance surrounding a maximum touches the edge of the image (edge of the selection does not matter). |
131 | 151 |
132 - **Light Background** - Select "yes" if the image background is brighter than the objects you want to find. | 152 - **Light Background** - Select "yes" if the image background is brighter than the objects you want to find. |
133 | 153 |
134 </help> | 154 </help> |
135 <expand macro="fiji_headless_citations" /> | 155 <expand macro="fiji_headless_citations"/> |
136 </tool> | 156 </tool> |