diff tomo_reconstruct.xml @ 21:3caba2116858 draft

"planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
author rv43
date Mon, 18 Apr 2022 19:43:15 +0000
parents 44f168e1e14f
children ef5c2f7b49ec
line wrap: on
line diff
--- a/tomo_reconstruct.xml	Mon Apr 18 18:10:07 2022 +0000
+++ b/tomo_reconstruct.xml	Mon Apr 18 19:43:15 2022 +0000
@@ -5,11 +5,12 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
+        mkdir center_slice_pngs;
         $__tool_directory__/tomo_reconstruct.py
         -i '$red_stacks'
         -c '$config'
         --center_offsets $center_offsets.lower_center_offset $center_offsets.upper_center_offset
-        --output_data 'output.npz'
+        --output_data 'output_data.npz'
         --output_config 'output_config.yaml'
         -l '$log'
     ]]></command>
@@ -24,6 +25,9 @@
     <outputs>
         <expand macro="common_outputs"/>
         <data name="output_data" format="npz" label="Reconstructed tomography stacks" from_work_dir="output_data.npz"/>
+        <collection name="recon_slices" type="list" label="Recontructed slices midway in each dimension">
+            <discover_datasets pattern="__name_and_ext__" directory="center_slice_pngs"/>
+        </collection>
     </outputs>
     <help><![CDATA[
         Reconstruct tomography images.