Mercurial > repos > ximgchess > chap_test_20230411
comparison tomo/tomo_reduce.xml @ 93:c63315c31cef draft
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit b682c580a95bebc59bc33128973cee4eac8362c7
| author | ximgchess |
|---|---|
| date | Wed, 24 May 2023 14:33:59 +0000 |
| parents | 142f73036013 |
| children | 3283cbddcc1d |
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| 92:142f73036013 | 93:c63315c31cef |
|---|---|
| 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 mkdir tomo_reduce_plots; |
| 10 #if str($map.type_selector) == "yaml" | 10 #if str($map.type_selector) == "yaml" |
| 11 $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' && | |
| 11 cp $input_file map.yaml && | 12 cp $input_file map.yaml && |
| 12 #if str($map.detector.type_selector) == "from_file" | 13 cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml && |
| 13 cat $map.detector.detector_file $tool_config > reduce.yaml && | |
| 14 #else | |
| 15 cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml && | |
| 16 #end if | |
| 17 #else | 14 #else |
| 18 cp $input_file setup.nex && | 15 cp $input_file setup.nex && |
| 19 cp $tool_config reduce.yaml && | 16 cp $tool_config reduce.yaml && |
| 20 #end if | 17 #end if |
| 21 CHAP --config | 18 CHAP --config |
| 47 <option value="nexus">NeXus</option> | 44 <option value="nexus">NeXus</option> |
| 48 </param> | 45 </param> |
| 49 <when value="yaml"> | 46 <when value="yaml"> |
| 50 <param name="input_file" type="data" format="yaml" optional="false" label="Map config file"/> | 47 <param name="input_file" type="data" format="yaml" optional="false" label="Map config file"/> |
| 51 <conditional name="detector"> | 48 <conditional name="detector"> |
| 52 <param name="type_selector" type="select" display="radio" label="Choose detector"> | 49 <param name="type_selector" type="select" display="radio" label="Choose detector prefix"> |
| 53 <option value="andor2.yaml">andor2</option> | 50 <option value="andor2.yaml">andor2</option> |
| 54 <option value="manta.yaml">manta</option> | 51 <option value="manta.yaml">manta</option> |
| 55 <option value="retiga.yaml">retiga</option> | 52 <option value="retiga.yaml">retiga</option> |
| 56 <option value="from_file">from file</option> | |
| 57 </param> | 53 </param> |
| 58 <when value="andor2.yaml"/> | 54 <when value="andor2.yaml"/> |
| 59 <when value="manta.yaml"/> | 55 <when value="manta.yaml"/> |
| 60 <when value="retiga.yaml"/> | 56 <when value="retiga.yaml"/> |
| 61 <when value="from_file"> | |
| 62 <param name="detector_file" type="data" format="yaml" optional="false" label="Detector config file"/> | |
| 63 </when> | |
| 64 </conditional> | 57 </conditional> |
| 65 </when> | 58 </when> |
| 66 <when value="nexus"> | 59 <when value="nexus"> |
| 67 <param name="input_file" type="data" format="nex" optional="false" label="Tomography setup file"/> | 60 <param name="input_file" type="data" format="nex" optional="false" label="Tomography setup file"/> |
| 68 </when> | 61 </when> |