Mercurial > repos > ximgchess > chap_test_20230411

annotate tomo/tomo_reconstruct.xml @ 124:020caca70a9a draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 6697892ecc504b00077394d0c167431ec3ac12f7-dirty
author ximgchess
date Tue, 30 May 2023 15:14:56 +0000
parents 66ffcd393336
children 1d40ef04d7ec
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1 <tool id="CHAP_tomo_reconstruct" name="Tomo Reconstruct" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
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2 <description>Reconstruct 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"/>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 mkdir tomo_reconstruct_plots;
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10 cp $input_file reduced.nex &&
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11 cp $center_file centers.yaml &&
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12 cp $tool_config reconstruct.yaml &&
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13 CHAP --config
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14 $__tool_directory__/pipeline_reconstruct.yaml
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15 ]]>
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16 </command>
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17 <configfiles>
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18 <configfile name="tool_config">
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19 <![CDATA[#slurp
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20 #if str($x_bounds.type_selector) == "enter_range"
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21 #echo 'x_bounds:' #
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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 #if str($y_bounds.type_selector) == "enter_range"
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26 #echo 'y_bounds:' #
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27 #echo '- ' + str($y_bounds.low) #
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28 #echo '- ' + str($y_bounds.upp) #
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29 #end if
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30 #echo 'secondary_iters: ' + str($secondary_iters) #
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31 #echo 'remove_stripe_sigma: ' + str($remove_stripe_sigma) #
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32 #echo 'ring_width: ' + str($ring_width) #
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33 ]]>
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34 </configfile>
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35 </configfiles>
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36 <inputs>
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37 <param name="input_file" type="data" format="nex" optional="false" label="Reduce tomography data file"/>
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38 <param name="center_file" type="data" format="yaml" optional="false" label="Rotation axis centers data file"/>
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39 <conditional name="x_bounds">
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40 <param name="type_selector" type="select" label="Choose reconstructed image range in the x-direction">
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41 <option value="full_range" selected="true">Use the full image range</option>
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42 <option value="enter_range">Manually enter the image range in the x-direction</option>
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43 </param>
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44 <when value="full_range"/>
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45 <when value="enter_range">
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46 <param name="low" type="integer" value="" optional="false" min="0" label="Lower image x-range index"/>
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47 <param name="upp" type="integer" value="" optional="false" min="0" label="Upper image x-range index"/>
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48 </when>
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49 </conditional>
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50 <conditional name="y_bounds">
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51 <param name="type_selector" type="select" label="Choose reconstructed image range in the y-direction">
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52 <option value="full_range" selected="true">Use the full image range</option>
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53 <option value="enter_range">Manually enter the image range in the y-direction</option>
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54 </param>
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55 <when value="full_range"/>
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56 <when value="enter_range">
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57 <param name="low" type="integer" value="" optional="false" min="0" label="Lower image y-range index"/>
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58 <param name="upp" type="integer" value="" optional="false" min="0" label="Upper image y-range index"/>
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59 </when>
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60 </conditional>
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61 <param name="secondary_iters" type="integer" value="0" optional="false" min="0" label="Number of secondary iterations"/>
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62 <param name="remove_stripe_sigma" type="float" value="0.05" optional="false" min="0" label="Damping parameter in horizontal stripe removal"/>
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63 <param name="ring_width" type="float" value="1" optional="false" min="1" label="Maximum filtered ring width in pixels"/>
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64 </inputs>
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65 <outputs>
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66 <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reconstruct.yaml" hidden="false"/>
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67 <collection name="tomo_reconstruct_plots" type="list" label="Data reconstruction images">
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68 <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/>
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69 </collection>
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70 <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
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71 </outputs>
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72 <help>
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73 <![CDATA[
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74 usage: PROG [-h] [--config CONFIG] [--verbose]
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75
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76 options:
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77 -h, --help show this help message and exit
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78 --config CONFIG Input configuration file
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79 --verbose verbose output
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80
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81 ]]>
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82 </help>
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83 <expand macro="citations"/>
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84 </tool>