Mercurial > repos > rv43 > tomo
view tomo_reconstruct.xml @ 68:ba5866d0251d draft
"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 3fde3e85030608a8a4d8e59308353b0144314dfe"
author | rv43 |
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date | Fri, 19 Aug 2022 20:16:56 +0000 |
parents | 26f99fdd8d61 |
children | d5e1d4ea2b7e |
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<tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.2.0" python_template_version="3.9"> <description>Perform a tomography reconstruction</description> <macros> <import>tomo_macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ mkdir center_slice_pngs; $__tool_directory__/tomo_reconstruct.py -i '$red_stacks' -c '$config' #if str($center_offsets.type_selector) == "offsets_manual" --center_offsets $center_offsets.lower_center_offset $center_offsets.upper_center_offset #end if --output_data 'output_data.npz' --output_config 'output_config.yaml' -l '$log' ]]></command> <inputs> <expand macro="common_inputs"/> <param name="red_stacks" type='data' format='npz' optional='false' label="Reduced stacks"/> <conditional name="center_offsets"> <param name="type_selector" type="select" label="Read reconstruction center axis offsets from file or enter enter manually"> <option value="offsets_from_file" selected="true">Read center axis offsets from file</option> <option value="offsets_manual">Manually enter center axis offsets</option> </param> <when value="offsets_from_file"/> <when value="offsets_manual"> <param name="lower_center_offset" type="float" value = "0" optional="false" label="Lower center offset"/> <param name="upper_center_offset" type="float" value = "0" optional="false" label="Upper center offset"/> </when> </conditional> </inputs> <outputs> <expand macro="common_outputs"/> <data name="output_data" format="npz" label="Reconstructed tomography stacks" from_work_dir="output_data.npz"/> <collection name="center_slice_pngs" type="list" label="Recontructed slices midway in each dimension"> <discover_datasets pattern="__name_and_ext__" directory="center_slice_pngs"/> </collection> <data name="output_config" format="tomo.config.yaml" label="Output config reconstruction" from_work_dir="output_config.yaml"/> </outputs> <help><![CDATA[ Reconstruct tomography images. ]]></help> <expand macro="citations"/> </tool>