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comparison tomo_reconstruct.xml @ 29:551d1ea2416d draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
author rv43
date Tue, 21 Mar 2023 18:46:02 +0000
parents 0891477bcb16
children 50923144fb56
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28:562fc79de827 29:551d1ea2416d
10 $__tool_directory__/tomo_reconstruct.py 10 $__tool_directory__/tomo_reconstruct.py
11 --input_file "$input_file" 11 --input_file "$input_file"
12 --center_file "$center_file" 12 --center_file "$center_file"
13 --output_file "output.nex" 13 --output_file "output.nex"
14 --galaxy_flag 14 --galaxy_flag
15 --x_bounds $x_bounds.low $x_bounds.upp 15 #if str($x_bounds.type_selector) == "enter_range"
16 --y_bounds $y_bounds.low $y_bounds.upp 16 --x_bounds $x_bounds.low $x_bounds.upp
17 #end if
18 #if str($y_bounds.type_selector) == "enter_range"
19 --y_bounds $y_bounds.low $y_bounds.upp
20 #end if
17 -l "$log" 21 -l "$log"
18 ]]> 22 ]]>
19 </command> 23 </command>
20 <inputs> 24 <inputs>
21 <param name="input_file" type="data" format="nex" optional="false" label="Reduced tomography data"/> 25 <param name="input_file" type="data" format="nex" optional="false" label="Reduced tomography data"/>
22 <param name="center_file" type="data" format="yaml" optional="false" label="Center axis input file"/> 26 <param name="center_file" type="data" format="yaml" optional="false" label="Center axis input file"/>
23 <section name="x_bounds" title="Boundaries of reconstructed images in x-direction"> 27 <conditional name="x_bounds">
24 <param name="low" type="integer" value="-1" label="Lower bound"/> 28 <param name="type_selector" type="select" label="Choose reconstructed image range in x-direction">
25 <param name="upp" type="integer" value="-1" label="Upper bound"/> 29 <option value="full_range" selected="true">Use the full image range</option>
26 </section> 30 <option value="enter_range">Manually enter the image range</option>
27 <section name="y_bounds" title="Boundaries of reconstructed images in y-direction"> 31 </param>
28 <param name="low" type="integer" value="-1" label="Lower bound"/> 32 <when value="full_range"/>
29 <param name="upp" type="integer" value="-1" label="Upper bound"/> 33 <when value="enter_range">
30 </section> 34 <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in x-direction"/>
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"/>
47 </when>
48 </conditional>
31 </inputs> 49 </inputs>
32 <outputs> 50 <outputs>
33 <expand macro="common_outputs"/> 51 <expand macro="common_outputs"/>
34 <collection name="tomo_reconstruct_plots" type="list" label="Data recontructed images"> 52 <collection name="tomo_reconstruct_plots" type="list" label="Data recontructed images">
35 <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/> 53 <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/>