Mercurial > repos > rv43 > tomo

annotate tomo_reconstruct.xml @ 75:d5e1d4ea2b7e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
75
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
1 <tool id="tomo_reconstruct" name="Tomo Reconstruction" version="1.0.0" python_template_version="3.9">
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
2 <description>Perform a tomography reconstruction</description>
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
3 <macros>
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
4 <import>tomo_macros.xml</import>
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
5 </macros>
75
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
6 <expand macro="requirements"/>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
7 <command detect_errors="exit_code">
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
8 <![CDATA[
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
9 mkdir tomo_reconstruct_plots;
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
10 $__tool_directory__/tomo_reconstruct.py
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
11 --input_file "$input_file"
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
12 --center_file "$center_file"
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
13 --output_file "output.nex"
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
14 --galaxy_flag
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
15 #if str($x_bounds.type_selector) == "enter_range"
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
16 --x_bounds $x_bounds.low $x_bounds.upp
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
17 #end if
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
18 #if str($y_bounds.type_selector) == "enter_range"
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
19 --y_bounds $y_bounds.low $y_bounds.upp
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
20 #end if
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
21 -l "$log"
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
22 ]]>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
23 </command>
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
24 <inputs>
75
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
25 <param name="input_file" type="data" format="nex" optional="false" label="Reduced tomography data"/>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
26 <param name="center_file" type="data" format="yaml" optional="false" label="Center axis input file"/>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
27 <conditional name="x_bounds">
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
28 <param name="type_selector" type="select" label="Choose reconstructed image range in x-direction">
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
29 <option value="full_range" selected="true">Use the full image range</option>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
30 <option value="enter_range">Manually enter the image range</option>
68
ba5866d0251d "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 3fde3e85030608a8a4d8e59308353b0144314dfe"
rv43
parents: 49
diff changeset
31 </param>
75
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
32 <when value="full_range"/>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
33 <when value="enter_range">
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
34 <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in x-direction"/>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
35 <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in x-direction"/>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
36 </when>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
37 </conditional>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
38 <conditional name="y_bounds">
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
39 <param name="type_selector" type="select" label="Choose reconstructed image range in y-direction">
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
40 <option value="full_range" selected="true">Use the full image range</option>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
41 <option value="enter_range">Manually enter the image range</option>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
42 </param>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
43 <when value="full_range"/>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
44 <when value="enter_range">
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
45 <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in y-direction"/>
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
46 <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in y-direction"/>
68
ba5866d0251d "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 3fde3e85030608a8a4d8e59308353b0144314dfe"
rv43
parents: 49
diff changeset
47 </when>
ba5866d0251d "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 3fde3e85030608a8a4d8e59308353b0144314dfe"
rv43
parents: 49
diff changeset
48 </conditional>
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
49 </inputs>
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
50 <outputs>
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
51 <expand macro="common_outputs"/>
75
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
52 <collection name="tomo_reconstruct_plots" type="list" label="Data recontruction images">
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
53 <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/>
21
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 16
diff changeset
54 </collection>
75
d5e1d4ea2b7e planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
rv43
parents: 68
diff changeset
55 <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
56 </outputs>
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
57 <help><![CDATA[
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
58 Reconstruct tomography images.
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
59 ]]></help>
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
60 <expand macro="citations"/>
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
61 </tool>