Mercurial > repos > ximgchess > chap_test_20230411

annotate tomo/tomo_find_center.xml @ 72:efb4a65f46eb draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 919e80fa3f8a9160766ff4d2c6b8956ec5553ad3-dirty
author ximgchess
date Mon, 24 Apr 2023 19:49:26 +0000
parents 0473fdc7f9b0
children 0476dee34886
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3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
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1 <tool id="CHAP_tomo_find_center" name="Tomo Find Center" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
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2 <description>Find rotation axis centers for the 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"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 mkdir tomo_find_center_plots;
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
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10 cp $input_file reduced.nex &&
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0473fdc7f9b0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 919e80fa3f8a9160766ff4d2c6b8956ec5553ad3-dirty
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11 cp $tool_config find_center.yaml &&
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3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
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12 CHAP --config
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
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13 $__tool_directory__/pipeline_find_center.yaml
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
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14 ]]>
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15 </command>
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16 <configfiles>
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17 <configfile name="tool_config">
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18 <![CDATA[#slurp
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19 #if str($center_rows.type_selector) == "full_range"
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
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20 #echo 'lower_row: -1' #
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21 #echo 'lower_row: -1' #
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22 #else
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
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23 #echo 'lower_row: ' + str($center_rows.low) #
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24 #echo 'lower_row: ' + str($center_rows.upp) #
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25 #end if
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
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26 ]]>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
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27 </configfile>
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28 </configfiles>
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29 <inputs>
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30 <param name="input_file" type="data" format="nex" optional="false" label="Reduce tomography data file"/>
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31 <conditional name="center_rows">
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32 <param name="type_selector" type="select" label="Choose axis center image rows">
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33 <option value="full_range" selected="true">Use the first and last detector row</option>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
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34 <option value="enter_range">Manually enter the center image rows</option>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
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35 </param>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
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36 <when value="full_range"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
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37 <when value="enter_range">
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38 <param name="low" type="integer" value="-1" optional="false" label="Lower detector row index"/>
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39 <param name="upp" type="integer" value="-1" optional="false" label="Upper detector row index"/>
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40 </when>
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41 </conditional>
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42 </inputs>
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43 <outputs>
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44 <data name="tool_config" format="yaml" label="Tool config" from_work_dir="find_center.yaml" hidden="false"/>
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45 <collection name="tomo_find_center_plots" type="list" label="Find rotation axis center images">
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46 <discover_datasets pattern="__name_and_ext__" directory="tomo_find_center_plots"/>
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47 </collection>
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48 <data name="output_file" format="yaml" label="Rotation axis centers data" from_work_dir="output.yaml"/>
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49 </outputs>
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50 <help>
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51 <![CDATA[
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52 usage: PROG [-h] [--config CONFIG] [--verbose]
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54 options:
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55 -h, --help show this help message and exit
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56 --config CONFIG Input configuration file
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57 --verbose verbose output
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58
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59 ]]>
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60 </help>
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61 <expand macro="citations"/>
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62 </tool>