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annotate tomo_reconstruct.xml @ 68:ba5866d0251d draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 3fde3e85030608a8a4d8e59308353b0144314dfe"
author rv43
date Fri, 19 Aug 2022 20:16:56 +0000
parents 26f99fdd8d61
children d5e1d4ea2b7e
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1 <tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.2.0" 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 '$config'
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12 #if str($center_offsets.type_selector) == "offsets_manual"
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13 --center_offsets $center_offsets.lower_center_offset $center_offsets.upper_center_offset
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14 #end if
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15 --output_data 'output_data.npz'
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16 --output_config 'output_config.yaml'
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17 -l '$log'
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18 ]]></command>
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19 <inputs>
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20 <expand macro="common_inputs"/>
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21 <param name="red_stacks" type='data' format='npz' optional='false' label="Reduced stacks"/>
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22 <conditional name="center_offsets">
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23 <param name="type_selector" type="select" label="Read reconstruction center axis offsets from file or enter enter manually">
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24 <option value="offsets_from_file" selected="true">Read center axis offsets from file</option>
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25 <option value="offsets_manual">Manually enter center axis offsets</option>
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26 </param>
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27 <when value="offsets_from_file"/>
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28 <when value="offsets_manual">
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29 <param name="lower_center_offset" type="float" value = "0" optional="false" label="Lower center offset"/>
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30 <param name="upper_center_offset" type="float" value = "0" optional="false" label="Upper center offset"/>
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31 </when>
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32 </conditional>
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33 </inputs>
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34 <outputs>
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35 <expand macro="common_outputs"/>
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36 <data name="output_data" format="npz" label="Reconstructed tomography stacks" from_work_dir="output_data.npz"/>
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37 <collection name="center_slice_pngs" type="list" label="Recontructed slices midway in each dimension">
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38 <discover_datasets pattern="__name_and_ext__" directory="center_slice_pngs"/>
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39 </collection>
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40 <data name="output_config" format="tomo.config.yaml" label="Output config reconstruction" from_work_dir="output_config.yaml"/>
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41 </outputs>
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42 <help><![CDATA[
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43 Reconstruct tomography images.
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44 ]]></help>
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45 <expand macro="citations"/>
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46 </tool>