make ThermoRawFileParser run parallel

.github/workflows/ci.yaml

@@ -112,14 +112,14 @@ jobs:
     # TODO this is only temporary and only for OpenMS
     - name: create test data
       run: |
+           echo '${{ needs.setup.outputs.repository-list }}' > repository_list.txt
            while read repo
            do
-               repo=$(dirname $(echo $repo | sed 's/\(^[^ ]\+\).*/\1/'))
                if [ -x $repo/test-data.sh ]; then
                    cd $repo
                    ./test-data.sh
                fi
-           done < tool_list_chunk.txt
+           done < repository_list.txt
     # TODO without this planemo task aborts with `System.IO.IOException: No space left on device` 
     #        sudo swapoff -a
     #        sudo rm -f /swapfile

.github/workflows/pr.yaml

@@ -240,17 +240,17 @@ jobs:
       with:
         path: ~/.planemo
         key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
-    # TODO this is only temporary and only for OpenMS
+#     # TODO this is only temporary and only for OpenMS
     - name: create test data
       run: |
+           echo '${{ needs.setup.outputs.repository-list }}' > repository_list.txt
            while read repo
            do
-               repo=$(dirname $(echo $repo | sed 's/\(^[^ ]\+\).*/\1/'))
                if [ -x $repo/test-data.sh ]; then
                    cd $repo
                    ./test-data.sh
                fi
-           done < tool_list_chunk.txt
+           done < repository_list.txt
     # TODO without this planemo task aborts with `System.IO.IOException: No space left on device` 
     #        sudo swapoff -a
     #        sudo rm -f /swapfile

tools/ThermoRawFileParser/.shed.yml

@@ -6,5 +6,5 @@ description: Thermo RAW file converter
 long_description: |
     Thermo RAW file converter based on the great ThermoRawFileParser project.
 homepage_url: https://github.com/compomics/ThermoRawFileParser
-remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser
+remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser
 type: unrestricted

tools/ThermoRawFileParser/test-data/really_small.json

@@ -0,0 +1 @@
+{"FileProperties":[{"accession":"NCIT:C47922","cvLabel":"NCIT","name":"Pathname","value":"really_small.raw"},{"accession":"NCIT:C25714","cvLabel":"NCIT","name":"Version","value":"66"},{"accession":"NCIT:C69199","cvLabel":"NCIT","name":"Content Creation Date","value":"03/25/2019 11:30:48"},{"accession":"NCIT:C25365","cvLabel":"NCIT","name":"Description","value":""}],"InstrumentProperties":[{"accession":"MS:1000494","cvLabel":"MS","name":"Thermo Scientific instrument model","value":"Orbitrap Fusion"},{"accession":"MS:1000496","cvLabel":"MS","name":"instrument attribute","value":"Orbitrap Fusion"},{"accession":"MS:1000529","cvLabel":"MS","name":"instrument serial number","value":"FSN10188"}],"MsData":[{"accession":"PRIDE:0000481","cvLabel":"PRIDE","name":"Number of MS1 spectra","value":"67"},{"accession":"PRIDE:0000482","cvLabel":"PRIDE","name":"Number of MS2 spectra","value":"34"},{"accession":"PRIDE:0000472","cvLabel":"PRIDE","name":"MS min charge","value":"2"},{"accession":"PRIDE:0000473","cvLabel":"PRIDE","name":"MS max charge","value":"3"},{"accession":"PRIDE:0000474","cvLabel":"PRIDE","name":"MS min RT","value":"0.89012589865"},{"accession":"PRIDE:0000475","cvLabel":"PRIDE","name":"MS max RT","value":"1.5947900096"},{"accession":"PRIDE:0000476","cvLabel":"PRIDE","name":"MS min MZ","value":"407.919311523438"},{"accession":"PRIDE:0000477","cvLabel":"PRIDE","name":"MS max MZ","value":"1138.40502929688"}],"SampleData":[],"ScanSettings":[{"accession":"MS:1000016","cvLabel":"MS","name":"scan start time","value":"0.89012589865"},{"accession":"MS:1000011","cvLabel":"MS","name":"mass resolution","value":"0.5"},{"accession":"UO:0000002","cvLabel":"MS","name":"mass unit","value":"None"},{"accession":"PRIDE:0000478","cvLabel":"PRIDE","name":"Number of scans","value":"101"},{"accession":"PRIDE:0000479","cvLabel":"PRIDE","name":"MS scan range","value":"1:101"},{"accession":"PRIDE:0000484","cvLabel":"PRIDE","name":"Retention time range","value":"0.89012589865:1.5947900096"},{"accession":"PRIDE:0000485","cvLabel":"PRIDE","name":"Mz range","value":"120:2000"},{"accession":"MS:1000422","cvLabel":"MS","name":"beam-type collision-induced dissociation","value":"HCD"}]}