Mercurial > repos > ximgchess > chap_test_20230411

annotate tomo/tomo_combine.xml @ 139:59d672fde7fd draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 3d091903055c4f157d9e266f8af0157fac1c95fd-dirty
author ximgchess
date Thu, 22 Jun 2023 14:45:11 +0000
parents 0bd8fb3aae96
children
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1 <tool id="CHAP_tomo_combine" name="Tomo Combine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
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2 <description>Combine tomography stacks</description>
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3 <macros>
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4 <import>../macros.xml</import>
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5 <import>tomo_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 mkdir tomo_combine_plots;
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11 cp $input_file reconstructed.nex &&
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12 cp $tool_config combine.yaml &&
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13 CHAP --config
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14 $__tool_directory__/pipeline_combine.yaml
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15 ]]>
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16 </command>
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17 <configfiles>
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18 <configfile name="tool_config">
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19 <![CDATA[#slurp
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20 #echo 'x_bounds:' #
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21 #if str($x_bounds.type_selector) == "enter_range"
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22 #echo '- ' + str($x_bounds.low) #
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23 #echo '- ' + str($x_bounds.upp) #
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24 #end if
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25 #echo 'y_bounds:' #
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26 #if str($y_bounds.type_selector) == "enter_range"
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27 #echo '- ' + str($y_bounds.low) #
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28 #echo '- ' + str($y_bounds.upp) #
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29 #end if
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30 ]]>
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31 </configfile>
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32 </configfiles>
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33 <inputs>
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34 <param name="input_file" type="data" format="nex" optional="false" label="Reconstructed tomography data file"/>
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35 <conditional name="x_bounds">
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36 <param name="type_selector" type="select" label="Choose combined image range in the x-direction">
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37 <option value="full_range" selected="true">Use the full image range</option>
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38 <option value="enter_range">Manually enter the image range in the x-direction</option>
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39 </param>
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40 <when value="full_range"/>
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41 <when value="enter_range">
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42 <param name="low" type="integer" value="" optional="false" min="0" label="Lower image x-range index"/>
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43 <param name="upp" type="integer" value="" optional="false" min="0" label="Upper image x-range index"/>
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44 </when>
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45 </conditional>
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46 <conditional name="y_bounds">
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47 <param name="type_selector" type="select" label="Choose combined image range in the y-direction">
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48 <option value="full_range" selected="true">Use the full image range</option>
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49 <option value="enter_range">Manually enter the image range in the y-direction</option>
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50 </param>
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51 <when value="full_range"/>
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52 <when value="enter_range">
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53 <param name="low" type="integer" value="" optional="false" min="0" label="Lower image y-range index"/>
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54 <param name="upp" type="integer" value="" optional="false" min="0" label="Upper image y-range index"/>
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55 </when>
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56 </conditional>
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57 </inputs>
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58 <outputs>
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59 <data name="tool_config" format="yaml" label="Tool config" from_work_dir="combine.yaml" hidden="false"/>
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60 <collection name="tomo_combine_plots" type="list" label="Data combination images">
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61 <discover_datasets pattern="__name_and_ext__" directory="tomo_combine_plots"/>
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62 </collection>
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63 <data name="output_file" format="nex" label="Combined tomography data" from_work_dir="output.nex"/>
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64 </outputs>
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65 <help>
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66 <![CDATA[
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67 usage: PROG [-h] [--config CONFIG] [--verbose]
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68
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69 options:
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70 -h, --help show this help message and exit
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71 --config CONFIG Input configuration file
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72 --verbose verbose output
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74 ]]>
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75 </help>
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76 <expand macro="citations"/>
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77 </tool>