Mercurial > repos > ximgchess > chap_test_20230411

comparison tomo/tomo_reduce.xml @ 60:3a9135044f14 draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit eda217fb0afe5af50380a24b578c668db9c004f4-dirty
author ximgchess
date Wed, 12 Apr 2023 19:04:05 +0000
parents 75199a75de43
children a560d5143348
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equal deleted inserted replaced
59:75199a75de43 60:3a9135044f14
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 $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' && 10 $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
10 ls -alh $__tool_directory__/.. && 11 #if str($map.type_selector) == "yaml"
11 cp $tool_config reduce.yaml 12 cp $input_file map.yaml &&
13 cat $__tool_directory__/andor2.yaml $tool_config > reduce.yaml &&
14 #else
15 cp $input_file setup.nex &&
16 cp $tool_config reduce.yaml &&
17 #end if
18 CHAP --config
19 #if str($map.type_selector) == "yaml"
20 $__tool_directory__/pipeline_reduce_yaml.yaml
21 #else
22 $__tool_directory__/pipeline_reduce_nexus.yaml
23 #end if
12 ]]> 24 ]]>
13 </command> 25 </command>
14 <configfiles> 26 <configfiles>
15 <configfile name="tool_config"> 27 <configfile name="tool_config">
16 <![CDATA[#slurp 28 <![CDATA[#slurp
17 #*
18 #if str($map.type_selector) == "yaml"
19 #echo 'detector:' #
20 #echo ' file: ' + str($__tool_directory__) + '/andor2.yaml' #
21 #end if
22 *#
23 #echo 'img_x_bounds:' # 29 #echo 'img_x_bounds:' #
24 #if str($img_x_bounds.type_selector) == "full_range" 30 #if str($img_x_bounds.type_selector) == "full_range"
25 #echo '- -1' # 31 #echo '- -1' #
26 #echo '- -1' # 32 #echo '- -1' #
27 #else 33 #else
66 </when> 72 </when>
67 </conditional> 73 </conditional>
68 </inputs> 74 </inputs>
69 <outputs> 75 <outputs>
70 <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reduce.yaml" hidden="false"/> 76 <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reduce.yaml" hidden="false"/>
77 <collection name="tomo_reduce_plots" type="list" label="Data reduction images">
78 <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/>
79 </collection>
80 <data name="output_file" format="nex" label="Reduced tomography data" from_work_dir="output.nex"/>
71 </outputs> 81 </outputs>
72 <help> 82 <help>
73 <![CDATA[ 83 <![CDATA[
74 usage: PROG [-h] [--config CONFIG] [--verbose] 84 usage: PROG [-h] [--config CONFIG] [--verbose]
75 85