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comparison imagej2_math.xml @ 3:d426c25946d4 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 16:11:17 +0000
parents d7fbe9662213
children
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2:d7fbe9662213 3:d426c25946d4
1 <tool id="imagej2_math" name="Operate on pixels" version="@WRAPPER_VERSION@.2"> 1 <tool id="imagej2_math" name="Operate on pixels" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>with ImageJ2</description> 2 <description>with ImageJ2</description>
3 <macros> 3 <macros>
4 <import>imagej2_macros.xml</import> 4 <import>imagej2_macros.xml</import>
5 </macros> 5 </macros>
6 <edam_operations> 6 <edam_operations>
11 <xref type="biii">imagej2</xref> 11 <xref type="biii">imagej2</xref>
12 </xrefs> 12 </xrefs>
13 <expand macro="fiji_requirements"/> 13 <expand macro="fiji_requirements"/>
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 #import os 15 #import os
16 #set error_log = 'output_log.txt'
17 touch '$error_log' &&
18 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0] 16 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
19 #set input_with_ext = '.'.join([input_sans_ext, $input.ext]) 17 #set input_with_ext = './' + '.'.join([input_sans_ext, $input.ext])
20 ln -s '$input.file_name' '$input_with_ext' && 18 ln -s '$input.file_name' '$input_with_ext' &&
21 #set output_filename = '.'.join(['output', $input.ext]) 19 #set output_filename = '.'.join(['output', $input.ext])
22 touch '$output_filename' && 20 touch '$output_filename' &&
23 ImageJ --ij2 --headless --debug 21 ImageJ --ij2 --headless --debug
24 --jython '$__tool_directory__/imagej2_math_jython_script.py' 22 --jython '$__tool_directory__/imagej2_math_jython_script.py'
25 '$error_log'
26 '$input_with_ext' 23 '$input_with_ext'
27 '$operation_cond.operation' 24 '$operation_cond.operation'
28 #if str($operation_cond.operation) == 'Macro': 25 #if str($operation_cond.operation) == 'Macro':
29 '$operation_cond.expression' 26 '$operation_cond.expression'
30 #else: 27 #else:
40 #else: 37 #else:
41 'None' 38 'None'
42 #end if 39 #end if
43 '$output_filename' 40 '$output_filename'
44 '$input.ext' 41 '$input.ext'
45 &>'$error_log'; 42 && mv '$output_filename' '$output'
46 if [[ $? -ne 0 ]]; then
47 cat '$error_log' >&2;
48 else
49 mv '$output_filename' '$output';
50 fi
51 ]]></command> 43 ]]></command>
52 <inputs> 44 <inputs>
53 <expand macro="param_input"/> 45 <expand macro="param_input"/>
54 <!-- 46 <!--
55 NOTE: The NaN Background option is not included here because it only works with 32-bit 47 NOTE: The NaN Background option is not included here because it only works with 32-bit
126 </outputs> 118 </outputs>
127 <tests> 119 <tests>
128 <test> 120 <test>
129 <param name="input" value="blobs.gif"/> 121 <param name="input" value="blobs.gif"/>
130 <param name="operation" value="Multiply"/> 122 <param name="operation" value="Multiply"/>
131 <output name="output" file="blobs_multiply.gif" compare="sim_size"/> 123 <output name="output" file="blobs_multiply.gif" compare="image_diff"/>
132 </test> 124 </test>
133 <test> 125 <test>
134 <param name="input" value="blobs.gif"/> 126 <param name="input" value="blobs.gif"/>
135 <param name="operation" value="Min"/> 127 <param name="operation" value="Min"/>
136 <param name="float_constant" value="255"/> 128 <param name="float_constant" value="255"/>
137 <output name="output" file="blobs_min.gif" compare="sim_size"/> 129 <output name="output" file="blobs_min.gif" compare="image_diff"/>
138 </test> 130 </test>
139 <test> 131 <test>
140 <param name="input" value="blobs.gif"/> 132 <param name="input" value="blobs.gif"/>
141 <param name="operation" value="Log"/> 133 <param name="operation" value="Log"/>
142 <output name="output" file="blobs_log.gif" compare="sim_size"/> 134 <output name="output" file="blobs_log.gif" compare="image_diff"/>
143 </test> 135 </test>
144 <test> 136 <test>
145 <param name="input" value="blobs.gif"/> 137 <param name="input" value="blobs.gif"/>
146 <param name="operation" value="Square"/> 138 <param name="operation" value="Square"/>
147 <output name="output" file="blobs_square.gif" compare="sim_size"/> 139 <output name="output" file="blobs_square.gif" compare="image_diff"/>
148 </test> 140 </test>
149 <test> 141 <test>
150 <param name="input" value="blobs.gif"/> 142 <param name="input" value="blobs.gif"/>
151 <param name="operation" value="Macro"/> 143 <param name="operation" value="Macro"/>
152 <output name="output" file="blobs_macro.gif" compare="sim_size"/> 144 <output name="output" file="blobs_macro.gif" compare="image_diff"/>
153 </test> 145 </test>
154 </tests> 146 </tests>
155 <help> 147 <help>
156 148
157 **What it does** 149 **What it does**