Mercurial > repos > rv43 > test_tomo_reconstruct

annotate tomo_reconstruct.xml @ 0:98e23dff1de2 draft default tip

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
author rv43
date Tue, 21 Mar 2023 16:22:42 +0000
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98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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1 <tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.3.0" python_template_version="3.9">
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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2 <description>Perform a tomography reconstruction</description>
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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3 <macros>
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4 <import>tomo_macros.xml</import>
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code">
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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8 <![CDATA[
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9 mkdir tomo_reconstruct_plots;
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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10 $__tool_directory__/tomo_reconstruct.py
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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11 --input_file "$input_file"
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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12 --center_file "$center_file"
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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13 --output_file "output.nex"
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14 --galaxy_flag
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15 -l "$log"
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16 ]]>
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17 </command>
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18 <inputs>
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19 <expand macro="common_inputs"/>
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20 <param name="input_file" type="data" format="nex" optional="false" label="Reduced tomography data"/>
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21 <param name="center_file" type="data" format="yaml" optional="false" label="Center axis input file"/>
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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22 </inputs>
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23 <outputs>
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24 <expand macro="common_outputs"/>
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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25 <collection name="tomo_reconstruct_plots" type="list" label="Data recontructed images">
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26 <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/>
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27 </collection>
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28 <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
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29 </outputs>
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30 <help><![CDATA[
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31 Reconstruct tomography images.
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32 ]]></help>
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33 <expand macro="citations"/>
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34 </tool>