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planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
author rv43
date Thu, 23 Mar 2023 13:39:14 +0000
parents ba5866d0251d
children
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1 <tool id="tomo_combine" name="Tomo Combine Reconstructed Stacks" version="1.0.0" python_template_version="3.9">
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2 <description>Combine reconstructed tomography stacks</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_combine_plots;
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10 $__tool_directory__/tomo_combine.py
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11 --input_file "$input_file"
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12 --output_file "output.nex"
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13 --galaxy_flag
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14 #if str($x_bounds.type_selector) == "enter_range"
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15 --x_bounds $x_bounds.low $x_bounds.upp
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16 #end if
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17 #if str($y_bounds.type_selector) == "enter_range"
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18 --y_bounds $y_bounds.low $y_bounds.upp
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19 #end if
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20 -l '$log'
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="input_file" type="data" format="nex" optional="false" label="Reconstructed tomography data"/>
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25 <conditional name="x_bounds">
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26 <param name="type_selector" type="select" label="Choose reconstructed image range in x-direction">
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27 <option value="full_range" selected="true">Use the full image range</option>
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28 <option value="enter_range">Manually enter the image range</option>
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29 </param>
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30 <when value="full_range"/>
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31 <when value="enter_range">
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32 <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in x-direction"/>
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33 <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in x-direction"/>
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34 </when>
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35 </conditional>
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36 <conditional name="y_bounds">
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37 <param name="type_selector" type="select" label="Choose reconstructed image range in y-direction">
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38 <option value="full_range" selected="true">Use the full image range</option>
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39 <option value="enter_range">Manually enter the image range</option>
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40 </param>
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41 <when value="full_range"/>
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42 <when value="enter_range">
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43 <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in y-direction"/>
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44 <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in y-direction"/>
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45 </when>
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46 </conditional>
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47 </inputs>
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48 <outputs>
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49 <expand macro="common_outputs"/>
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50 <collection name="tomo_combine_plots" type="list" label="Combine recontructed data images">
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51 <discover_datasets pattern="__name_and_ext__" directory="tomo_combine_plots"/>
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52 </collection>
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53 <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
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54 </outputs>
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55 <help><![CDATA[
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56 Combine reconstructed tomography images.
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57 ]]></help>
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58 <expand macro="citations"/>
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59 </tool>