Mercurial > repos > rv43 > chess_tomo

annotate tomo_reconstruct.xml @ 18:dee0b25fcabe draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
author rv43
date Tue, 21 Mar 2023 15:35:48 +0000
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18
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1 <tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.3.0" 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">
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8 <![CDATA[
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9 mkdir center_slice_pngs;
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10 $__tool_directory__/tomo_reconstruct.py
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11 --input_file '$input_file'
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12 --center_file '$center_file'
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13 --output_file 'output.nex'
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14 --galaxy_flag
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15 #if str($center_offsets.type_selector) == "offsets_manual"
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16 --center_offsets $center_offsets.low $center_offsets.upp
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17 #end if
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18 -l '$log'
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19 ]]>
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20 </command>
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21 <inputs>
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22 <expand macro="common_inputs"/>
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23 <param name="input_file" type='data' format='nex' optional='false' label="Reduced tomography data"/>
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24 <param name="center_file" type='data' format='yaml' optional='false' label="Center axis input file"/>
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25 <conditional name="center_offsets">
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26 <param name="type_selector" type="select" label="Read reconstruction center axis offsets from file or enter enter manually">
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27 <option value="offsets_from_file" selected="true">Read center axis offsets from file</option>
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28 <option value="offsets_manual">Manually enter center axis offsets</option>
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29 </param>
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30 <when value="offsets_from_file"/>
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31 <when value="offsets_manual">
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32 <param name="low" type="float" value = "0" optional="false" label="Lower center offset"/>
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33 <param name="upp" type="float" value = "0" optional="false" label="Upper center offset"/>
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34 </when>
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35 </conditional>
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36 </inputs>
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37 <outputs>
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38 <expand macro="common_outputs"/>
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39 <collection name="center_slice_pngs" type="list" label="Recontructed slices midway in each dimension">
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40 <discover_datasets pattern="__name_and_ext__" directory="center_slice_pngs"/>
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41 </collection>
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42 <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
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43 </outputs>
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44 <help><![CDATA[
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45 Reconstruct tomography images.
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46 ]]></help>
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47 <expand macro="citations"/>
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48 </tool>