Mercurial > repos > rv43 > chess_tomo

annotate tomo_reconstruct.xml @ 33:50923144fb56 draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
author rv43
date Wed, 22 Mar 2023 16:46:26 +0000
parents 551d1ea2416d
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1 <tool id="tomo_reconstruct" name="Tomo Reconstruction" version="1.0.0" 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 "$center_file"
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13 --output_file "output.nex"
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14 --galaxy_flag
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15 #if str($x_bounds.type_selector) == "enter_range"
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16 --x_bounds $x_bounds.low $x_bounds.upp
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17 #end if
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18 #if str($y_bounds.type_selector) == "enter_range"
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19 --y_bounds $y_bounds.low $y_bounds.upp
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20 #end if
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21 -l "$log"
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22 ]]>
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23 </command>
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24 <inputs>
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25 <param name="input_file" type="data" format="nex" optional="false" label="Reduced tomography data"/>
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26 <param name="center_file" type="data" format="yaml" optional="false" label="Center axis input file"/>
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27 <conditional name="x_bounds">
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28 <param name="type_selector" type="select" label="Choose reconstructed image range in x-direction">
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29 <option value="full_range" selected="true">Use the full image range</option>
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30 <option value="enter_range">Manually enter the image range</option>
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31 </param>
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32 <when value="full_range"/>
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33 <when value="enter_range">
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34 <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in x-direction"/>
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35 <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in x-direction"/>
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36 </when>
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37 </conditional>
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38 <conditional name="y_bounds">
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39 <param name="type_selector" type="select" label="Choose reconstructed image range in y-direction">
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40 <option value="full_range" selected="true">Use the full image range</option>
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41 <option value="enter_range">Manually enter the image range</option>
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42 </param>
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43 <when value="full_range"/>
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44 <when value="enter_range">
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45 <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in y-direction"/>
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46 <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in y-direction"/>
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47 </when>
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48 </conditional>
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49 </inputs>
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50 <outputs>
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51 <expand macro="common_outputs"/>
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52 <collection name="tomo_reconstruct_plots" type="list" label="Data recontruction images">
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53 <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/>
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54 </collection>
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55 <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
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56 </outputs>
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57 <help><![CDATA[
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58 Reconstruct tomography images.
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59 ]]></help>
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60 <expand macro="citations"/>
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61 </tool>