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annotate tomo_reduce.xml @ 75:d5e1d4ea2b7e draft default tip

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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 4f4ee8db5f67
children
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1 <tool id="tomo_reduce" name="Tomo Reduce" version="1.0.0" python_template_version="3.9">
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2 <description>Reduce 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">
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8 <![CDATA[
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9 mkdir tomo_reduce_plots;
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10 $__tool_directory__/tomo_reduce.py
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11 --input_file "$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($station.type_selector) == "id3b"
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15 #if str($station.img_bounds.type_selector) == "enter_range"
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16 --img_x_bounds $station.img_bounds.low $station.img_bounds.upp
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17 #end if
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18 #end if
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19 -l "$log"
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20 ]]>
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21 </command>
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22 <inputs>
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23 <param name="input_file" type="data" optional="false" label="Input file"/>
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24 <conditional name="station">
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25 <param name="type_selector" type="select" display="radio" label="Choose station">
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26 <option value="id3a" selected="true">id3a (SMB)</option>
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27 <option value="id3b">id3b (FMB)</option>
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28 </param>
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29 <when value="id3a"/>
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30 <when value="id3b">
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31 <conditional name="img_bounds">
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32 <param name="type_selector" type="select" display="radio" label="Choose image range for data reduction">
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33 <option value="enter_range" selected="true">Manually enter the image range</option>
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34 <option value="full_range">Use the full image range</option>
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35 </param>
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36 <when value="enter_range">
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37 <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in vertical direction"/>
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38 <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in vertical direction"/>
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39 </when>
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40 <when value="full_range"/>
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41 </conditional>
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42 </when>
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43 </conditional>
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44 </inputs>
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45 <outputs>
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46 <expand macro="common_outputs"/>
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47 <collection name="tomo_reduce_plots" type="list" label="Data reduction images">
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48 <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/>
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49 </collection>
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50 <data name="output_file" format="nex" label="Reduced tomography data" from_work_dir="output.nex"/>
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51 </outputs>
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52 <help>
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53 <![CDATA[
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54 Reduce tomography images.
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55 ]]>
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56 </help>
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57 <expand macro="citations"/>
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58 </tool>