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annotate tomo_reconstruct.xml @ 24:0891477bcb16 draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
author rv43
date Tue, 21 Mar 2023 17:40:36 +0000
parents fbbd82938303
children 551d1ea2416d
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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 tomo_reconstruct_plots;
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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 --x_bounds $x_bounds.low $x_bounds.upp
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16 --y_bounds $y_bounds.low $y_bounds.upp
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17 -l "$log"
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param name="input_file" type="data" format="nex" optional="false" label="Reduced tomography data"/>
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22 <param name="center_file" type="data" format="yaml" optional="false" label="Center axis input file"/>
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23 <section name="x_bounds" title="Boundaries of reconstructed images in x-direction">
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24 <param name="low" type="integer" value="-1" label="Lower bound"/>
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25 <param name="upp" type="integer" value="-1" label="Upper bound"/>
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26 </section>
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27 <section name="y_bounds" title="Boundaries of reconstructed images in y-direction">
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28 <param name="low" type="integer" value="-1" label="Lower bound"/>
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29 <param name="upp" type="integer" value="-1" label="Upper bound"/>
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30 </section>
22
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31 </inputs>
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32 <outputs>
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33 <expand macro="common_outputs"/>
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34 <collection name="tomo_reconstruct_plots" type="list" label="Data recontructed images">
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35 <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/>
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36 </collection>
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37 <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
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38 </outputs>
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39 <help><![CDATA[
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40 Reconstruct tomography images.
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41 ]]></help>
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42 <expand macro="citations"/>
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43 </tool>