Mercurial > repos > ximgchess > chap_test_20230411

annotate tomo/tomo_reconstruct.xml @ 104:5d0c96f9c0ff draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 6697892ecc504b00077394d0c167431ec3ac12f7-dirty
author ximgchess
date Thu, 25 May 2023 12:44:16 +0000
parents efb4a65f46eb
children d523d6396e58
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
66
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
1 <tool id="CHAP_tomo_reconstruct" name="Tomo Reconstruct" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
2 <description>Reconstruct tomography stacks</description>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
3 <macros>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
4 <import>tomo_macros.xml</import>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
5 </macros>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
6 <expand macro="requirements"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
7 <command detect_errors="exit_code">
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
8 <![CDATA[
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
9 mkdir tomo_reconstruct_plots;
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
10 cp $input_file reduced.nex &&
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
11 cp $center_file centers.yaml &&
71
0473fdc7f9b0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 919e80fa3f8a9160766ff4d2c6b8956ec5553ad3-dirty
ximgchess
parents: 66
diff changeset
12 cp $tool_config reconstruct.yaml &&
66
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
13 CHAP --config
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
14 $__tool_directory__/pipeline_reconstruct.yaml
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
15 ]]>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
16 </command>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
17 <configfiles>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
18 <configfile name="tool_config">
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
19 <![CDATA[#slurp
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
20 #echo 'x_bounds:' #
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
21 #if str($x_bounds.type_selector) == "full_range"
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
22 #echo '- -1' #
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
23 #echo '- -1' #
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
24 #else
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
25 #echo '- ' + str($x_bounds.low) #
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
26 #echo '- ' + str($x_bounds.upp) #
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
27 #end if
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
28 #echo 'y_bounds:' #
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
29 #if str($y_bounds.type_selector) == "full_range"
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
30 #echo '- -1' #
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
31 #echo '- -1' #
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
32 #else
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
33 #echo '- ' + str($y_bounds.low) #
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
34 #echo '- ' + str($y_bounds.upp) #
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
35 #end if
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
36 ]]>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
37 </configfile>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
38 </configfiles>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
39 <inputs>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
40 <param name="input_file" type="data" format="nex" optional="false" label="Reduce tomography data file"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
41 <param name="center_file" type="data" format="yaml" optional="false" label="Rotation axis centers data file"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
42 <conditional name="x_bounds">
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
43 <param name="type_selector" type="select" label="Choose reconstructed image range in the x-direction">
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
44 <option value="full_range" selected="true">Use the full image range</option>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
45 <option value="enter_range">Manually enter the image range in the x-direction</option>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
46 </param>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
47 <when value="full_range"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
48 <when value="enter_range">
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
49 <param name="low" type="integer" value="-1" optional="false" label="Lower image x-range index"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
50 <param name="upp" type="integer" value="-1" optional="false" label="Upper image x-range index"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
51 </when>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
52 </conditional>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
53 <conditional name="y_bounds">
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
54 <param name="type_selector" type="select" label="Choose reconstructed image range in the y-direction">
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
55 <option value="full_range" selected="true">Use the full image range</option>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
56 <option value="enter_range">Manually enter the image range in the y-direction</option>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
57 </param>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
58 <when value="full_range"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
59 <when value="enter_range">
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
60 <param name="low" type="integer" value="-1" optional="false" label="Lower image y-range index"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
61 <param name="upp" type="integer" value="-1" optional="false" label="Upper image y-range index"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
62 </when>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
63 </conditional>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
64 </inputs>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
65 <outputs>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
66 <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reconstruct.yaml" hidden="false"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
67 <collection name="tomo_reconstruct_plots" type="list" label="Data reconstruction images">
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
68 <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
69 </collection>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
70 <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
71 </outputs>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
72 <help>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
73 <![CDATA[
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
74 usage: PROG [-h] [--config CONFIG] [--verbose]
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
75
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
76 options:
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
77 -h, --help show this help message and exit
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
78 --config CONFIG Input configuration file
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
79 --verbose verbose output
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
80
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
81 ]]>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
82 </help>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
83 <expand macro="citations"/>
3b1dbe3fb91b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 922ced93dce7a89190712f1ad9abad569fe52683
ximgchess
parents:
diff changeset
84 </tool>