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annotate tomo_setup.xml @ 11:ec7c3e84d611 draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7"
author rv43
date Fri, 08 Apr 2022 16:39:07 +0000
parents 845270a96464
children 4eba03628711
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1 <tool id="tomo_setup" name="Tomo Setup" version="0.1.1" python_template_version="3.9">
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2 <description>Preprocess tomography images</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 cp '$inputfiles' inputfiles.txt &&
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9 $__tool_directory__/tomo_setup.py
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10 -i inputfiles.txt
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11 -c '$config'
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12 --theta_range '$thetas.theta_start $thetas.theta_end $thetas.num_thetas'
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13 --dark 'dark_field.png'
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14 --bright 'bright_field.png'
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15 --tomo 'tomo.png'
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16 --detectorbounds 'detectorbounds.png'
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17 --output_data 'output.npz'
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18 --output_config 'output_config.yaml'
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19 -l '$log'
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20 #for $s in $tomo_sets# ${s.offset} ${s.num} #end for
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21 ]]></command>
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22 <configfiles>
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23 <configfile name="inputfiles"><![CDATA[#slurp
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24 #for $s in $tomo_sets
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25 #for $input in $s.inputs
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26 #echo str($input) + '\t' + $input.element_identifier #
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27 #end for
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28 #end for
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29 ]]></configfile>
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30 </configfiles>
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31 <inputs>
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32 <expand macro="common_inputs"/>
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33 <section name="thetas" title="Tomography angles">
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34 <param name="theta_start" type="float" min="0.0" max="360.0" value="0.0" label="Lower bound"/>
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35 <param name="theta_end" type="float" min="0.0" max="360.0" value="0.0" label="Upper bound"/>
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36 <param name="num_thetas" type="integer" min="1" value="1" label="Number of angles"/>
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37 </section>
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38 <repeat name='tomo_sets' title="Tomography image sets">
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39 <param name="inputs" type="data_collection" label="Image file collection"/>
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40 <param name="offset" type="integer" min="0" value="0" label="Image index offset"/>
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41 <param name="num" type="integer" min="1" value="1" label="Number of images"/>
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42 </repeat>
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43 </inputs>
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44 <outputs>
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45 <expand macro="common_outputs"/>
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46 <data name="inputfiles" format="txt" label="Input files" from_work_dir="inputfiles.txt" hidden="true"/>
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47 <data name="dark_field" format="png" label="Dark field" from_work_dir="dark_field.png"/>
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48 <data name="bright_field" format="png" label="Bright field" from_work_dir="bright_field.png"/>
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49 <data name="tomo" format="png" label="First tomography image" from_work_dir="tomo.png"/>
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50 <data name="detectorbounds" format="png" label="Detector bounds" from_work_dir="detectorbounds.png"/>
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51 <data name="output_data" format="npz" label="Preprocessed tomography data" from_work_dir="output_data.npz"/>
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52 </outputs>
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53 <help><![CDATA[
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54 Preprocess tomography images.
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55 ]]></help>
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56 <expand macro="citations"/>
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57 </tool>