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comparison tomo_reconstruct.xml @ 18:dee0b25fcabe draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
author rv43
date Tue, 21 Mar 2023 15:35:48 +0000
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17:e89919e468cd 18:dee0b25fcabe
1 <tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.3.0" python_template_version="3.9">
2 <description>Perform a tomography reconstruction</description>
3 <macros>
4 <import>tomo_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 mkdir center_slice_pngs;
10 $__tool_directory__/tomo_reconstruct.py
11 --input_file '$input_file'
12 --center_file '$center_file'
13 --output_file 'output.nex'
14 --galaxy_flag
15 #if str($center_offsets.type_selector) == "offsets_manual"
16 --center_offsets $center_offsets.low $center_offsets.upp
17 #end if
18 -l '$log'
19 ]]>
20 </command>
21 <inputs>
22 <expand macro="common_inputs"/>
23 <param name="input_file" type='data' format='nex' optional='false' label="Reduced tomography data"/>
24 <param name="center_file" type='data' format='yaml' optional='false' label="Center axis input file"/>
25 <conditional name="center_offsets">
26 <param name="type_selector" type="select" label="Read reconstruction center axis offsets from file or enter enter manually">
27 <option value="offsets_from_file" selected="true">Read center axis offsets from file</option>
28 <option value="offsets_manual">Manually enter center axis offsets</option>
29 </param>
30 <when value="offsets_from_file"/>
31 <when value="offsets_manual">
32 <param name="low" type="float" value = "0" optional="false" label="Lower center offset"/>
33 <param name="upp" type="float" value = "0" optional="false" label="Upper center offset"/>
34 </when>
35 </conditional>
36 </inputs>
37 <outputs>
38 <expand macro="common_outputs"/>
39 <collection name="center_slice_pngs" type="list" label="Recontructed slices midway in each dimension">
40 <discover_datasets pattern="__name_and_ext__" directory="center_slice_pngs"/>
41 </collection>
42 <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
43 </outputs>
44 <help><![CDATA[
45 Reconstruct tomography images.
46 ]]></help>
47 <expand macro="citations"/>
48 </tool>