Mercurial > repos > ximgchess > chap_test_20230411

annotate tomo/tomo_reduce.xml @ 137:0bd8fb3aae96 draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
author ximgchess
date Tue, 20 Jun 2023 18:13:36 +0000
parents 49985da419b8
children
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1 <tool id="CHAP_tomo_reduce" name="Tomo Reduce" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
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2 <description>Reduce tomography images</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_reduce_plots;
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11 #if str($map.type_selector) == "yaml"
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12 cp $input_file map.yaml &&
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13 #if str($map.detector.type_selector) == "from_file"
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14 cat $map.detector.detector_file $tool_config > reduce.yaml &&
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15 #elif str($map.detector.type_selector) == "manual"
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16 cat $tool_config > reduce.yaml &&
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17 #else
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18 cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml &&
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19 #end if
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20 #else
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21 cp $input_file setup.nex &&
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22 cp $tool_config reduce.yaml &&
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23 #end if
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24 CHAP --config
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25 #if str($map.type_selector) == "yaml"
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26 $__tool_directory__/pipeline_reduce_yaml.yaml
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27 #else
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28 $__tool_directory__/pipeline_reduce_nexus.yaml
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29 #end if
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30 ]]>
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31 </command>
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32 <configfiles>
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33 <configfile name="tool_config">
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34 <![CDATA[#slurp
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35 #if str($map.detector.type_selector) == "manual"
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36 #echo 'detector:' #
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37 #echo ' prefix: ' + str($map.detector.prefix) #
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38 #echo ' rows: ' + str($map.detector.rows) #
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39 #echo ' columns: ' + str($map.detector.columns) #
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40 #echo ' pixel_size:' #
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41 #echo ' - ' + str($map.detector.x_pixelsize) #
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42 #echo ' - ' + str($map.detector.y_pixelsize) #
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43 #echo ' lens_magnification: ' + str($map.detector.lens_magnification) #
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44 #end if
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45 #echo 'img_x_bounds:' #
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46 #if str($img_x_bounds.type_selector) == "enter_range"
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47 #echo '- ' + str($img_x_bounds.low) #
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48 #echo '- ' + str($img_x_bounds.upp) #
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49 #end if
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50 ]]>
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51 </configfile>
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52 </configfiles>
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53 <inputs>
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54 <conditional name="map">
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55 <param name="type_selector" type="select" display="radio" label="Choose map file type">
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56 <option value="yaml">YAML</option>
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57 <option value="nexus">NeXus</option>
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58 </param>
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59 <when value="yaml">
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60 <param name="input_file" type="data" format="yaml" optional="false" label="Map config file"/>
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61 <conditional name="detector">
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62 <param name="type_selector" type="select" display="radio" label="Choose detector">
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63 <option value="andor2.yaml">andor2</option>
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64 <option value="manta.yaml">manta</option>
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65 <option value="retiga.yaml">retiga</option>
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66 <option value="manual">enter manually</option>
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67 <option value="from_file">from file</option>
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68 </param>
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69 <when value="andor2.yaml"/>
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70 <when value="manta.yaml"/>
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71 <when value="retiga.yaml"/>
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72 <when value="manual">
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73 <param name="prefix" type="text" label="Detector prefix in SPEC file"/>
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74 <param name="rows" type="integer" value="" optional="false" min="1" label="Number of pixel rows on detector"/>
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75 <param name="columns" type="integer" value="" optional="false" min="1" label="Number of pixel columns on detector"/>
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76 <param name="x_pixelsize" type="float" value="" optional="false" min="0.0" label="Row pixel size of detector in mm"/>
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77 <param name="y_pixelsize" type="float" value="" optional="false" min="0.0" label="Column pixel size of detector in mm"/>
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78 <param name="lens_magnification" type="float" value="1.0" optional="true" label="Detector lens magnification"/>
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79 </when>
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80 <when value="from_file">
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81 <param name="detector_file" type="data" format="yaml" optional="false" label="Detector config file"/>
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82 </when>
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83 </conditional>
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84 </when>
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85 <when value="nexus">
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86 <param name="input_file" type="data" format="nex" optional="false" label="Tomography setup file"/>
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87 </when>
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88 </conditional>
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89 <conditional name="img_x_bounds">
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90 <param name="type_selector" type="select" label="Choose vertical detector image bounds">
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91 <option value="full_range" selected="true">Use the full image range</option>
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92 <option value="enter_range">Manually enter the image range</option>
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93 </param>
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94 <when value="full_range"/>
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95 <when value="enter_range">
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96 <param name="low" type="integer" value="" optional="false" min="0" label="Lower image range index"/>
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97 <param name="upp" type="integer" value="" optional="false" min="0" label="Upper image range index"/>
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98 </when>
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99 </conditional>
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100 </inputs>
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101 <outputs>
9
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102 <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reduce.yaml" hidden="false"/>
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103 <collection name="tomo_reduce_plots" type="list" label="Data reduction images">
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104 <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/>
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105 </collection>
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106 <data name="output_file" format="nex" label="Reduced tomography data" from_work_dir="output.nex"/>
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107 </outputs>
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108 <help>
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109 <![CDATA[
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110 usage: PROG [-h] [--config CONFIG] [--verbose]
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111
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112 options:
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113 -h, --help show this help message and exit
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114 --config CONFIG Input configuration file
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115 --verbose verbose output
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116
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117 ]]>
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118 </help>
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119 <expand macro="citations"/>
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120 </tool>