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annotate tomo_setup.xml @ 1:e4778148df6b draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
author rv43
date Thu, 31 Mar 2022 18:24:16 +0000
parents cb1b0d757704
children b8977c98800b
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1 <tool id="tomo_setup" name="Tomo Setup" version="0.1.0" python_template_version="3.9">
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2 <description>Preprocess tomography images</description>
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3 <requirements>
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4 <requirement type="package" version="1.11.0">tomopy</requirement>
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5 <requirement type="package" version="3.6.0">h5py</requirement>
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6 </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_data'
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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 <param name="config" type='data' format='yaml' optional='false' label="Input config"/>
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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 <data name="inputfiles" format="txt" label="Input files" from_work_dir="inputfiles.txt" hidden="true"/>
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46 <data name="dark_field" format="png" label="Dark field" from_work_dir="dark_field.png"/>
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47 <data name="bright_field" format="png" label="Bright field" from_work_dir="bright_field.png"/>
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48 <data name="tomo" format="png" label="First tomography image" from_work_dir="tomo.png"/>
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49 <data name="detectorbounds" format="png" label="Detector bounds" from_work_dir="detectorbounds.png"/>
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50 <data name="output_data" format="npz" label="Preprocessed tomography data"/>
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51 <data name="output_config" format="yaml" label="Output config" from_work_dir="output_config.yaml"/>
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52 <data name="log" format="txt" label="Log"/>
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53 </outputs>
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54 <help><![CDATA[
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55 Preprocess tomography images.
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56 ]]></help>
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57 <citations>
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58 <citation type="bibtex">
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59 @misc{githubsum_files,
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60 author = {Verberg, Rolf},
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61 year = {2022},
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62 title = {Tomo Setup},
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63 publisher = {GitHub},
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64 journal = {GitHub repository},
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65 url = {somewhere},
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66 }</citation>
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67 </citations>
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68
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69 </tool>