Mercurial > repos > imgteam > segmetrics
changeset 5:ac55e2f4d9e3 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
| author | imgteam |
|---|---|
| date | Mon, 13 Nov 2023 22:12:16 +0000 |
| parents | 7989264b5780 |
| children | 462f49860277 |
| files | segmetrics.xml |
| diffstat | 1 files changed, 41 insertions(+), 38 deletions(-) [+] |
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--- a/segmetrics.xml Tue Jun 20 21:40:31 2023 +0000 +++ b/segmetrics.xml Mon Nov 13 22:12:16 2023 +0000 @@ -1,43 +1,46 @@ -<tool id="ip_segmetrics" name="SegMetrics" version="1.4.0-1" profile="20.05"> - <description>image segmentation and object detection performance measures</description> - <requirements> +<tool id="ip_segmetrics" name="Compute image segmentation and object detection performance measures" version="1.4.0-2" profile="20.05"> + <description>with SegMetrics</description> + <edam_operations> + <edam_operation>operation_3443</edam_operation> + </edam_operations> + <requirements> <requirement type="package" version="1.4">segmetrics</requirement> <requirement type="package" version="0.23.4">pandas</requirement> - </requirements> - <command detect_errors="aggressive"> - <![CDATA[ - python '$__tool_directory__/run-segmetrics.py' - '$input_seg' - '$input_gt' - ./results.tsv - $unzip - $is_seg_unique - $is_gt_unique - #for $m in $measures - #set $kwargs = '' - #set $suffix = '' - #set $is_distance = False - #if str($m.measure_type.measure_type_selector) == 'ISBIScore': - #set $kwargs = 'min_ref_size=' + str($m.measure_type.min_ref_size) + ', ' - #elif str($m.measure_type.measure_type_selector) == 'Hausdorff': - #set $kwargs = 'mode="' + str($m.measure_type.mode) + '", quantile=' + str($m.measure_type.quantile) + ', ' - #set $is_distance = True - #elif str($m.measure_type.measure_type_selector) == 'NSD': - #set $is_distance = True - #end if - #if $is_distance: - #if $m.measure_type.object_based: - #set $suffix = '.object_based()' - #end if - #end if - #if str($m.measure_type.aggregation) != '': - #set $kwargs = 'aggregation="' + str($m.measure_type.aggregation) + '", ' + $kwargs - #end if - 'sm.${m.measure_type.measure_type_selector}(${kwargs})${suffix}' - #end for - ]]> - </command> - <inputs> + </requirements> + <command detect_errors="aggressive"> + <![CDATA[ + python '$__tool_directory__/run-segmetrics.py' + '$input_seg' + '$input_gt' + ./results.tsv + $unzip + $is_seg_unique + $is_gt_unique + #for $m in $measures + #set $kwargs = '' + #set $suffix = '' + #set $is_distance = False + #if str($m.measure_type.measure_type_selector) == 'ISBIScore': + #set $kwargs = 'min_ref_size=' + str($m.measure_type.min_ref_size) + ', ' + #elif str($m.measure_type.measure_type_selector) == 'Hausdorff': + #set $kwargs = 'mode="' + str($m.measure_type.mode) + '", quantile=' + str($m.measure_type.quantile) + ', ' + #set $is_distance = True + #elif str($m.measure_type.measure_type_selector) == 'NSD': + #set $is_distance = True + #end if + #if $is_distance: + #if $m.measure_type.object_based: + #set $suffix = '.object_based()' + #end if + #end if + #if str($m.measure_type.aggregation) != '': + #set $kwargs = 'aggregation="' + str($m.measure_type.aggregation) + '", ' + $kwargs + #end if + 'sm.${m.measure_type.measure_type_selector}(${kwargs})${suffix}' + #end for + ]]> + </command> + <inputs> <param name="input_seg" type="data" format="tiff,png,zip" label="Segmented images" /> <param name="input_gt" type="data" format="tiff,png,zip" label="Ground truth images" />