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comparison tomo_reconstruct.xml @ 21:3caba2116858 draft

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"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
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20:c033f8843dc0 21:3caba2116858
3 <macros> 3 <macros>
4 <import>tomo_macros.xml</import> 4 <import>tomo_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 mkdir center_slice_pngs;
8 $__tool_directory__/tomo_reconstruct.py 9 $__tool_directory__/tomo_reconstruct.py
9 -i '$red_stacks' 10 -i '$red_stacks'
10 -c '$config' 11 -c '$config'
11 --center_offsets $center_offsets.lower_center_offset $center_offsets.upper_center_offset 12 --center_offsets $center_offsets.lower_center_offset $center_offsets.upper_center_offset
12 --output_data 'output.npz' 13 --output_data 'output_data.npz'
13 --output_config 'output_config.yaml' 14 --output_config 'output_config.yaml'
14 -l '$log' 15 -l '$log'
15 ]]></command> 16 ]]></command>
16 <inputs> 17 <inputs>
17 <expand macro="common_inputs"/> 18 <expand macro="common_inputs"/>
22 </section> 23 </section>
23 </inputs> 24 </inputs>
24 <outputs> 25 <outputs>
25 <expand macro="common_outputs"/> 26 <expand macro="common_outputs"/>
26 <data name="output_data" format="npz" label="Reconstructed tomography stacks" from_work_dir="output_data.npz"/> 27 <data name="output_data" format="npz" label="Reconstructed tomography stacks" from_work_dir="output_data.npz"/>
28 <collection name="recon_slices" type="list" label="Recontructed slices midway in each dimension">
29 <discover_datasets pattern="__name_and_ext__" directory="center_slice_pngs"/>
30 </collection>
27 </outputs> 31 </outputs>
28 <help><![CDATA[ 32 <help><![CDATA[
29 Reconstruct tomography images. 33 Reconstruct tomography images.
30 ]]></help> 34 ]]></help>
31 <expand macro="citations"/> 35 <expand macro="citations"/>