Mercurial > repos > ximgchess > chap_test_20230411
comparison tomo/tomo_reconstruct.xml @ 121:d523d6396e58 draft
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 6697892ecc504b00077394d0c167431ec3ac12f7-dirty
| author | ximgchess |
|---|---|
| date | Tue, 30 May 2023 14:52:07 +0000 |
| parents | efb4a65f46eb |
| children | 66ffcd393336 |
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| 120:00eb84d2c84a | 121:d523d6396e58 |
|---|---|
| 16 </command> | 16 </command> |
| 17 <configfiles> | 17 <configfiles> |
| 18 <configfile name="tool_config"> | 18 <configfile name="tool_config"> |
| 19 <![CDATA[#slurp | 19 <![CDATA[#slurp |
| 20 #echo 'x_bounds:' # | 20 #echo 'x_bounds:' # |
| 21 #if str($x_bounds.type_selector) == "full_range" | 21 #if str($x_bounds.type_selector) == "enter_range" |
| 22 #echo '- -1' # | |
| 23 #echo '- -1' # | |
| 24 #else | |
| 25 #echo '- ' + str($x_bounds.low) # | 22 #echo '- ' + str($x_bounds.low) # |
| 26 #echo '- ' + str($x_bounds.upp) # | 23 #echo '- ' + str($x_bounds.upp) # |
| 27 #end if | 24 #end if |
| 28 #echo 'y_bounds:' # | 25 #echo 'y_bounds:' # |
| 29 #if str($y_bounds.type_selector) == "full_range" | 26 #if str($y_bounds.type_selector) == "enter_range" |
| 30 #echo '- -1' # | |
| 31 #echo '- -1' # | |
| 32 #else | |
| 33 #echo '- ' + str($y_bounds.low) # | 27 #echo '- ' + str($y_bounds.low) # |
| 34 #echo '- ' + str($y_bounds.upp) # | 28 #echo '- ' + str($y_bounds.upp) # |
| 35 #end if | 29 #end if |
| 30 #echo 'secondary_iters: ' + str($secondary_iters) # | |
| 31 #echo 'remove_stripe_sigma: ' + str($remove_stripe_sigma) # | |
| 32 #echo 'ring_width: ' + str($ring_width) # | |
| 36 ]]> | 33 ]]> |
| 37 </configfile> | 34 </configfile> |
| 38 </configfiles> | 35 </configfiles> |
| 39 <inputs> | 36 <inputs> |
| 40 <param name="input_file" type="data" format="nex" optional="false" label="Reduce tomography data file"/> | 37 <param name="input_file" type="data" format="nex" optional="false" label="Reduce tomography data file"/> |
| 44 <option value="full_range" selected="true">Use the full image range</option> | 41 <option value="full_range" selected="true">Use the full image range</option> |
| 45 <option value="enter_range">Manually enter the image range in the x-direction</option> | 42 <option value="enter_range">Manually enter the image range in the x-direction</option> |
| 46 </param> | 43 </param> |
| 47 <when value="full_range"/> | 44 <when value="full_range"/> |
| 48 <when value="enter_range"> | 45 <when value="enter_range"> |
| 49 <param name="low" type="integer" value="-1" optional="false" label="Lower image x-range index"/> | 46 <param name="low" type="integer" value="" optional="false" min="0" label="Lower image x-range index"/> |
| 50 <param name="upp" type="integer" value="-1" optional="false" label="Upper image x-range index"/> | 47 <param name="upp" type="integer" value="" optional="false" min="0" label="Upper image x-range index"/> |
| 51 </when> | 48 </when> |
| 52 </conditional> | 49 </conditional> |
| 53 <conditional name="y_bounds"> | 50 <conditional name="y_bounds"> |
| 54 <param name="type_selector" type="select" label="Choose reconstructed image range in the y-direction"> | 51 <param name="type_selector" type="select" label="Choose reconstructed image range in the y-direction"> |
| 55 <option value="full_range" selected="true">Use the full image range</option> | 52 <option value="full_range" selected="true">Use the full image range</option> |
| 56 <option value="enter_range">Manually enter the image range in the y-direction</option> | 53 <option value="enter_range">Manually enter the image range in the y-direction</option> |
| 57 </param> | 54 </param> |
| 58 <when value="full_range"/> | 55 <when value="full_range"/> |
| 59 <when value="enter_range"> | 56 <when value="enter_range"> |
| 60 <param name="low" type="integer" value="-1" optional="false" label="Lower image y-range index"/> | 57 <param name="low" type="integer" value="" optional="false" min="0" label="Lower image y-range index"/> |
| 61 <param name="upp" type="integer" value="-1" optional="false" label="Upper image y-range index"/> | 58 <param name="upp" type="integer" value="" optional="false" min="0" label="Upper image y-range index"/> |
| 62 </when> | 59 </when> |
| 63 </conditional> | 60 </conditional> |
| 61 <param name="secondary_iters" type="int" value="0" optional="false" min="0" label="Number of secondary iterations"/> | |
| 62 <param name="remove_stripe_sigma" type="float" value="0.05" optional="false" min="0" label="Damping parameter in horizontal stripe removal"/> | |
| 63 <param name="ring_width" type="float" value="1" optional="false" min="1" label="Maximum filtered ring width in pixels"/> | |
| 64 </inputs> | 64 </inputs> |
| 65 <outputs> | 65 <outputs> |
| 66 <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reconstruct.yaml" hidden="false"/> | 66 <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reconstruct.yaml" hidden="false"/> |
| 67 <collection name="tomo_reconstruct_plots" type="list" label="Data reconstruction images"> | 67 <collection name="tomo_reconstruct_plots" type="list" label="Data reconstruction images"> |
| 68 <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/> | 68 <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/> |