Mercurial > repos > ximgchess > chap_test_20230411

annotate tomo/tomo_reduce.xml @ 4:ed26d2bb9723 draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 3e8c1c54d5e12fdbc4f6c5cdae88b6d054db7c45-dirty
author ximgchess
date Tue, 11 Apr 2023 20:02:52 +0000
parents a865a7d1cd91
children 47a0648cdfd1
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84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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1 <tool id="CHAP_tomo_reduce" name="Tomo Reduce" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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2 <description>Reduce tomography images</description>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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3 <macros>
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4 <import>tomo_macros.xml</import>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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5 </macros>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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6 <expand macro="requirements"/>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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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;
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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10 pip --exists-action i install certif-pyspec==1.5.3 &&
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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11 #if str($map.type_selector) == "YAML"
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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12 cp '$input_file' map.yaml &&
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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13 #else
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14 cp '$input_file' setup.nex &&
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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15 #end if
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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16 cp '$tool_config' reduce.yaml &&
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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17 CHAP --config
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18 #if str($map.type_selector) == "YAML"
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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19 '$__tool_directory__/pipeline_reduce_yaml.yaml'
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20 #else
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21 '$__tool_directory__/pipeline_reduce_nexus.yaml'
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22 #end if
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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23 ]]>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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24 </command>
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25 <configfiles>
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26 <configfile name="tool_config">
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27 <![CDATA[#slurp
3
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28 #if str($map.type_selector) == "YAML"
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ed26d2bb9723 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 3e8c1c54d5e12fdbc4f6c5cdae88b6d054db7c45-dirty
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29 #cat andor2.yaml
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30 #end if
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31 #echo 'img_x_bounds:' #
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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32 #if str($img_x_bounds.type_selector) == "full_range"
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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33 #echo '- -1'
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34 #echo '- -1'
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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35 #else
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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36 #echo '- ' + str($img_x_bounds.low)
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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37 #echo '- ' + str($img_x_bounds.upp)
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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38 #end if
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39 ]]>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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40 </configfile>
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41 </configfiles>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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42 <inputs>
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43 <conditional name="map">
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44 <param name="type_selector" type="select" display="radio" label="Choose map file type">
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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45 <option value="yaml">YAML</option>
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46 <option value="nexus">NeXus</option>
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47 </param>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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48 <when value="yaml">
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49 <param name="input_file" type="data" format="yaml" optional="false" label="Map config file"/>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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50 <conditional name="detector">
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51 <param name="type_selector" type="select" display="radio" label="Choose detector prefix">
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52 <option value="andor2">andor2</option>
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53 <option value="manta">manta</option>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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54 <option value="retiga">retiga</option>
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55 </param>
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56 <when value="andor2"/>
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57 <when value="manta"/>
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58 <when value="retiga"/>
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59 </conditional>
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60 </when>
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61 <when value="nexus">
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62 <param name="input_file" type="data" format="nex" optional="false" label="Tomography setup file"/>
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63 </when>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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64 </conditional>
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65 <conditional name="img_x_bounds">
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66 <param name="type_selector" type="select" label="Choose vertical detector image bounds">
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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67 <option value="full_range" selected="true">Use the full image range</option>
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68 <option value="enter_range">Manually enter the image range</option>
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69 </param>
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70 <when value="full_range"/>
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71 <when value="enter_range">
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72 <param name="low" type="integer" value="-1" optional="false" label="Lower image range index"/>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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73 <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index"/>
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74 </when>
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75 </conditional>
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76 </inputs>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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77 <outputs>
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78 <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reduce.yaml" hidden="false"/>
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79 <collection name="tomo_reduce_plots" type="list" label="Data reduction images">
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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80 <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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81 </collection>
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82 <data name="output_file" format="nex" label="Reduced tomography data" from_work_dir="output.nex"/>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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83 </outputs>
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84 <help>
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85 <![CDATA[
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86 usage: PROG [-h] [--config CONFIG] [--verbose]
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87
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88 options:
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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89 -h, --help show this help message and exit
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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90 --config CONFIG Input configuration file
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91 --verbose verbose output
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92
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93 ]]>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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94 </help>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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95 <expand macro="citations"/>
84a215623d9e planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a
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96 </tool>