Mercurial > repos > rv43 > chess_tomo

annotate tomo_combine.xml @ 35:e6bf49af75bc 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 19fefed1d90e6d214dc6eb6998ad11eee8233f24-dirty
author rv43
date Wed, 22 Mar 2023 16:52:56 +0000
parents 50923144fb56
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
33
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
1 <tool id="tomo_combine" name="Tomo Combine Reconstructed Stacks" version="1.0.0" python_template_version="3.9">
30
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
2 <description>Combine reconstructed tomography stacks</description>
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
3 <macros>
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
4 <import>tomo_macros.xml</import>
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
5 </macros>
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
6 <expand macro="requirements" />
33
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
7 <command detect_errors="exit_code">
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
8 <![CDATA[
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
9 mkdir tomo_combine_plots;
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
10 $__tool_directory__/tomo_combine.py
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
11 --input_file "$input_file"
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
12 --output_file "output.nex"
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
13 --galaxy_flag
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
14 #if str($x_bounds.type_selector) == "enter_range"
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
15 --x_bounds $x_bounds.low $x_bounds.upp
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
16 #end if
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
17 #if str($y_bounds.type_selector) == "enter_range"
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
18 --y_bounds $y_bounds.low $y_bounds.upp
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
19 #end if
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
20 -l '$log'
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
21 ]]>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
22 </command>
30
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
23 <inputs>
33
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
24 <param name="input_file" type="data" format="nex" optional="false" label="Reconstructed tomography data"/>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
25 <conditional name="x_bounds">
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
26 <param name="type_selector" type="select" label="Choose reconstructed image range in x-direction">
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
27 <option value="full_range" selected="true">Use the full image range</option>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
28 <option value="enter_range">Manually enter the image range</option>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
29 </param>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
30 <when value="full_range"/>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
31 <when value="enter_range">
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
32 <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in x-direction"/>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
33 <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in x-direction"/>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
34 </when>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
35 </conditional>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
36 <conditional name="y_bounds">
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
37 <param name="type_selector" type="select" label="Choose reconstructed image range in y-direction">
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
38 <option value="full_range" selected="true">Use the full image range</option>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
39 <option value="enter_range">Manually enter the image range</option>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
40 </param>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
41 <when value="full_range"/>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
42 <when value="enter_range">
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
43 <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in y-direction"/>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
44 <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in y-direction"/>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
45 </when>
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
46 </conditional>
30
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
47 </inputs>
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
48 <outputs>
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
49 <expand macro="common_outputs"/>
33
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
50 <collection name="tomo_combine_plots" type="list" label="Combine recontructed data images">
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
51 <discover_datasets pattern="__name_and_ext__" directory="tomo_combine_plots"/>
30
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
52 </collection>
33
50923144fb56 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
rv43
parents: 31
diff changeset
53 <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
30
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
54 </outputs>
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
55 <help><![CDATA[
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
56 Combine reconstructed tomography images.
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
57 ]]></help>
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
58 <expand macro="citations"/>
3342c0518d4c planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
59 </tool>