Mercurial > repos > iuc > imagej2_analyze_skeleton
diff imagej2_analyze_skeleton.xml @ 2:9631aab7da53 draft
planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
| author | iuc |
|---|---|
| date | Wed, 26 Aug 2015 14:36:10 -0400 |
| parents | dd8e4e000d2f |
| children | 20555566d6ad |
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--- a/imagej2_analyze_skeleton.xml Tue Aug 04 13:19:34 2015 -0400 +++ b/imagej2_analyze_skeleton.xml Wed Aug 26 14:36:10 2015 -0400 @@ -1,26 +1,27 @@ <?xml version='1.0' encoding='UTF-8'?> -<tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="1.0.0"> +<tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.0"> <description>with ImageJ2</description> <macros> <import>imagej2_macros.xml</import> </macros> - <expand macro="fiji_20141125_requirements" /> + <expand macro="fiji_requirements" /> <command> <![CDATA[ python $__tool_directory__/imagej2_analyze_skeleton.py --input "$input" --input_datatype $input.ext + --black_background $black_background --prune_cycle_method $prune_cycle_method --prune_ends $prune_ends --calculate_largest_shortest_path $calculate_largest_shortest_path - --show_detailed_info $show_detailed_info - @max_heap_size_args@ + ##TODO: seel below--show_detailed_info $show_detailed_info --jython_script $__tool_directory__/jython_script.py --output "$output" ]]> </command> <inputs> <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select grayscale image"/> + <expand macro="black_background_param" /> <param name="prune_cycle_method" type="select" label="Prune cycle method"> <option value="none" selected="True">None</option> <option value="shortest_branch">Shortest branch</option> @@ -35,11 +36,13 @@ <option value="no" selected="True">No</option> <option value="yes">Yes</option> </param> + <!-- TODO: Uncomment this option when the tool has been enhanced to use the + future "Display labeled skeletons" option. See http://fiji.sc/AnalyzeSkeleton. <param name="show_detailed_info" type="select" label="Show detailed info"> <option value="no" selected="True">No</option> <option value="yes">Yes</option> </param> - <expand macro="max_heap_size_type_conditional" /> + --> </inputs> <outputs> <data name="output" format="tabular" label="${tool.name} on ${on_string}" /> @@ -63,9 +66,12 @@ <output name="output" file="largest_shortest_path_basic.tabular" ftype="tabular" /> </test> <test> + <!-- TODO: Change this test and the following test to set "show_detailed_info" + to "yes" when the tool has been enhanced to use the future "Display labeled skeletons" + option. See http://fiji.sc/AnalyzeSkeleton. --> <param name="input" value="skeletonized_blobs.gif" /> <param name="input_datatype" value="gif" /> - <param name="show_detailed_info" value="yes" /> + <!-- <param name="show_detailed_info" value="yes" /> --> <output name="output" file="detailed.tabular" ftype="tabular" /> </test> <test> @@ -73,7 +79,7 @@ <param name="input_datatype" value="jpg" /> <param name="prune_cycle_method" value="shortest_branch" /> <param name="calculate_largest_shortest_path" value="yes" /> - <param name="show_detailed_info" value="yes" /> + <!-- <param name="show_detailed_info" value="yes" /> --> <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular" /> </test> </tests> @@ -112,7 +118,6 @@ - **Prune cycle method**: prune the possible loops in the skeleton. - **Prune ends**: prunes any branch that ends in an end-point. - **Calculate largest shortest path**: calculate the largest shortest path of each skeleton using the APSP (all pairs shortest path). -- **Show detailed info**: produces information about the branches of each skeleton in the image. ]]> </help> <citations>
