Mercurial > repos > ximgchess > chap_test_20230411

comparison tomo/tomo_reduce.xml @ 43:5d3313dbb8a2 draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit eda217fb0afe5af50380a24b578c668db9c004f4-dirty
author ximgchess
date Wed, 12 Apr 2023 14:31:08 +0000
parents 7c2b2bb53c23
children b5871d66b242
comparison
equal deleted inserted replaced
42:7c2b2bb53c23 43:5d3313dbb8a2
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 pip --exists-action i install --target /nfs/chess/galaxy-dev/var/dependencies/_conda/envs certif-pyspec==1.5.3 && 9 mkdir tomo_reduce_plots;
10 cp $tool_config reduce.yaml 10 #if str($map.type_selector) == "yaml"
11 cp $input_file map.yaml &&
12 cat $__tool_directory__/andor2.yaml $tool_config > reduce.yaml &&
13 #else
14 cp $input_file setup.nex &&
15 cp $tool_config reduce.yaml &&
16 #end if
17 CHAP --config
18 #if str($map.type_selector) == "yaml"
19 $__tool_directory__/pipeline_reduce_yaml.yaml
20 #else
21 $__tool_directory__/pipeline_reduce_nexus.yaml
22 #end if
11 ]]> 23 ]]>
12 </command> 24 </command>
13 <configfiles> 25 <configfiles>
14 <configfile name="tool_config"> 26 <configfile name="tool_config">
15 <![CDATA[#slurp 27 <![CDATA[#slurp
65 </when> 77 </when>
66 </conditional> 78 </conditional>
67 </inputs> 79 </inputs>
68 <outputs> 80 <outputs>
69 <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reduce.yaml" hidden="false"/> 81 <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reduce.yaml" hidden="false"/>
82 <collection name="tomo_reduce_plots" type="list" label="Data reduction images">
83 <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/>
84 </collection>
85 <data name="output_file" format="nex" label="Reduced tomography data" from_work_dir="output.nex"/>
70 </outputs> 86 </outputs>
71 <help> 87 <help>
72 <![CDATA[ 88 <![CDATA[
73 usage: PROG [-h] [--config CONFIG] [--verbose] 89 usage: PROG [-h] [--config CONFIG] [--verbose]
74 90