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comparison tomo_reconstruct.xml @ 75:d5e1d4ea2b7e draft default tip

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
author rv43
date Thu, 23 Mar 2023 13:39:14 +0000
parents ba5866d0251d
children
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equal deleted inserted replaced
74:4f4ee8db5f67 75:d5e1d4ea2b7e
1 <tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.2.0" python_template_version="3.9"> 1 <tool id="tomo_reconstruct" name="Tomo Reconstruction" version="1.0.0" python_template_version="3.9">
2 <description>Perform a tomography reconstruction</description> 2 <description>Perform a tomography reconstruction</description>
3 <macros> 3 <macros>
4 <import>tomo_macros.xml</import> 4 <import>tomo_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code">
8 mkdir center_slice_pngs; 8 <![CDATA[
9 $__tool_directory__/tomo_reconstruct.py 9 mkdir tomo_reconstruct_plots;
10 -i '$red_stacks' 10 $__tool_directory__/tomo_reconstruct.py
11 -c '$config' 11 --input_file "$input_file"
12 #if str($center_offsets.type_selector) == "offsets_manual" 12 --center_file "$center_file"
13 --center_offsets $center_offsets.lower_center_offset $center_offsets.upper_center_offset 13 --output_file "output.nex"
14 #end if 14 --galaxy_flag
15 --output_data 'output_data.npz' 15 #if str($x_bounds.type_selector) == "enter_range"
16 --output_config 'output_config.yaml' 16 --x_bounds $x_bounds.low $x_bounds.upp
17 -l '$log' 17 #end if
18 ]]></command> 18 #if str($y_bounds.type_selector) == "enter_range"
19 --y_bounds $y_bounds.low $y_bounds.upp
20 #end if
21 -l "$log"
22 ]]>
23 </command>
19 <inputs> 24 <inputs>
20 <expand macro="common_inputs"/> 25 <param name="input_file" type="data" format="nex" optional="false" label="Reduced tomography data"/>
21 <param name="red_stacks" type='data' format='npz' optional='false' label="Reduced stacks"/> 26 <param name="center_file" type="data" format="yaml" optional="false" label="Center axis input file"/>
22 <conditional name="center_offsets"> 27 <conditional name="x_bounds">
23 <param name="type_selector" type="select" label="Read reconstruction center axis offsets from file or enter enter manually"> 28 <param name="type_selector" type="select" label="Choose reconstructed image range in x-direction">
24 <option value="offsets_from_file" selected="true">Read center axis offsets from file</option> 29 <option value="full_range" selected="true">Use the full image range</option>
25 <option value="offsets_manual">Manually enter center axis offsets</option> 30 <option value="enter_range">Manually enter the image range</option>
26 </param> 31 </param>
27 <when value="offsets_from_file"/> 32 <when value="full_range"/>
28 <when value="offsets_manual"> 33 <when value="enter_range">
29 <param name="lower_center_offset" type="float" value = "0" optional="false" label="Lower center offset"/> 34 <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in x-direction"/>
30 <param name="upper_center_offset" type="float" value = "0" optional="false" label="Upper center offset"/> 35 <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in x-direction"/>
36 </when>
37 </conditional>
38 <conditional name="y_bounds">
39 <param name="type_selector" type="select" label="Choose reconstructed image range in y-direction">
40 <option value="full_range" selected="true">Use the full image range</option>
41 <option value="enter_range">Manually enter the image range</option>
42 </param>
43 <when value="full_range"/>
44 <when value="enter_range">
45 <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in y-direction"/>
46 <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in y-direction"/>
31 </when> 47 </when>
32 </conditional> 48 </conditional>
33 </inputs> 49 </inputs>
34 <outputs> 50 <outputs>
35 <expand macro="common_outputs"/> 51 <expand macro="common_outputs"/>
36 <data name="output_data" format="npz" label="Reconstructed tomography stacks" from_work_dir="output_data.npz"/> 52 <collection name="tomo_reconstruct_plots" type="list" label="Data recontruction images">
37 <collection name="center_slice_pngs" type="list" label="Recontructed slices midway in each dimension"> 53 <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/>
38 <discover_datasets pattern="__name_and_ext__" directory="center_slice_pngs"/>
39 </collection> 54 </collection>
40 <data name="output_config" format="tomo.config.yaml" label="Output config reconstruction" from_work_dir="output_config.yaml"/> 55 <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
41 </outputs> 56 </outputs>
42 <help><![CDATA[ 57 <help><![CDATA[
43 Reconstruct tomography images. 58 Reconstruct tomography images.
44 ]]></help> 59 ]]></help>
45 <expand macro="citations"/> 60 <expand macro="citations"/>