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comparison tomo_reduce.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 4f4ee8db5f67
children
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74:4f4ee8db5f67 75:d5e1d4ea2b7e
1 <tool id="tomo_reduce" name="Tomo Reduce" version="0.1.0" python_template_version="3.9"> 1 <tool id="tomo_reduce" name="Tomo Reduce" version="1.0.0" python_template_version="3.9">
2 <description>Reduce tomography images</description> 2 <description>Reduce tomography images</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"> 7 <command detect_errors="exit_code">
8 <![CDATA[ 8 <![CDATA[
9 mkdir tomo_reduce_plots; 9 mkdir tomo_reduce_plots;
10 $__tool_directory__/tomo_reduce.py 10 $__tool_directory__/tomo_reduce.py
11 --input_file '$input_file' 11 --input_file "$input_file"
12 --output_file 'output.nxs' 12 --output_file "output.nex"
13 --galaxy_flag 13 --galaxy_flag
14 --img_x_bounds $x_bounds.x_bound_low $x_bounds.x_bound_upp 14 #if str($station.type_selector) == "id3b"
15 -l '$log' 15 #if str($station.img_bounds.type_selector) == "enter_range"
16 --img_x_bounds $station.img_bounds.low $station.img_bounds.upp
17 #end if
18 #end if
19 -l "$log"
16 ]]> 20 ]]>
17 </command> 21 </command>
18 <inputs> 22 <inputs>
19 <param name="input_file" type="data" optional="false" label="Input file"/> 23 <param name="input_file" type="data" optional="false" label="Input file"/>
24 <conditional name="station">
25 <param name="type_selector" type="select" display="radio" label="Choose station">
26 <option value="id3a" selected="true">id3a (SMB)</option>
27 <option value="id3b">id3b (FMB)</option>
28 </param>
29 <when value="id3a"/>
30 <when value="id3b">
31 <conditional name="img_bounds">
32 <param name="type_selector" type="select" display="radio" label="Choose image range for data reduction">
33 <option value="enter_range" selected="true">Manually enter the image range</option>
34 <option value="full_range">Use the full image range</option>
35 </param>
36 <when value="enter_range">
37 <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in vertical direction"/>
38 <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in vertical direction"/>
39 </when>
40 <when value="full_range"/>
41 </conditional>
42 </when>
43 </conditional>
20 </inputs> 44 </inputs>
21 <outputs> 45 <outputs>
22 <expand macro="common_outputs"/> 46 <expand macro="common_outputs"/>
23 <collection name="tomo_reduce_plots" type="list" label="Tomo data reduction images"> 47 <collection name="tomo_reduce_plots" type="list" label="Data reduction images">
24 <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/> 48 <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/>
25 </collection> 49 </collection>
26 <data name="output_file" format="nxs" label="Reduced tomography data" from_work_dir="output.nxs"/> 50 <data name="output_file" format="nex" label="Reduced tomography data" from_work_dir="output.nex"/>
27 </outputs> 51 </outputs>
28 <help> 52 <help>
29 <![CDATA[ 53 <![CDATA[
30 Reduce tomography images. 54 Reduce tomography images.
31 ]]> 55 ]]>