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annotate tomo_reconstruct.xml @ 23:3e336f5b6402 draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit e023f10ae8d507a19015a033e176cb973262ab6e"
author rv43
date Mon, 18 Apr 2022 20:02:08 +0000
parents 3caba2116858
children ef5c2f7b49ec
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1 <tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.1.0" python_template_version="3.9">
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2 <description>Perform a tomography reconstruction</description>
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3 <macros>
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4 <import>tomo_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 mkdir center_slice_pngs;
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9 $__tool_directory__/tomo_reconstruct.py
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10 -i '$red_stacks'
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11 -c '$config'
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12 --center_offsets $center_offsets.lower_center_offset $center_offsets.upper_center_offset
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13 --output_data 'output_data.npz'
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14 --output_config 'output_config.yaml'
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15 -l '$log'
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16 ]]></command>
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17 <inputs>
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18 <expand macro="common_inputs"/>
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19 <param name="red_stacks" type='data' format='npz' optional='false' label="Reduced stacks"/>
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20 <section name="center_offsets" title="Reconstruction center axis offsets">
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21 <param name="lower_center_offset" type="float" value = "0" optional="false" label="Lower center offset"/>
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22 <param name="upper_center_offset" type="float" value = "0" optional="false" label="Upper center offset"/>
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23 </section>
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24 </inputs>
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25 <outputs>
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26 <expand macro="common_outputs"/>
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27 <data name="output_data" format="npz" label="Reconstructed tomography stacks" from_work_dir="output_data.npz"/>
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28 <collection name="recon_slices" type="list" label="Recontructed slices midway in each dimension">
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29 <discover_datasets pattern="__name_and_ext__" directory="center_slice_pngs"/>
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30 </collection>
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31 </outputs>
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32 <help><![CDATA[
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33 Reconstruct tomography images.
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34 ]]></help>
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35 <expand macro="citations"/>
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36 </tool>