diff --git a/tools/rcx-tk/.shed.yml b/tools/rcx-tk/.shed.yml new file mode 100644 index 00000000..3f7829f2 --- /dev/null +++ b/tools/rcx-tk/.shed.yml @@ -0,0 +1,9 @@ +name: rcx_tk +owner: recetox +remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/" +homepage_url: "https://github.com/RECETOX/rcx-tk" +categories: + - Metabolomics +description: "Tools to process metadata or alkane files." +long_description: "rcx-tk package provides tools to process the metadata or alkane files. On the input, the user is expected to supply a path to the metadata/alkane file in tsv/csv/xls/xlsx file. The file is then converted to a dataframe which is further processed. The main steps are columns rearrangement, validation of the file names and derivation of new metadata: sampleName, sequenceIdentifier, sampleIdentifier and localOrder. Finally, the processed dataframe is saved into user-defined location." +type: unrestricted \ No newline at end of file diff --git a/tools/rcx-tk/rcx-tk.xml b/tools/rcx-tk/rcx-tk.xml new file mode 100644 index 00000000..40e2c55c --- /dev/null +++ b/tools/rcx-tk/rcx-tk.xml @@ -0,0 +1,74 @@ + + + topic_3172 + topic_0091 + topic_3520 + + + operation_0336 + operation_3695 + + + rcx-tk + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.5281/zenodo.4471245 + + \ No newline at end of file diff --git a/tools/rcx-tk/test-data/input_alkanes.txt b/tools/rcx-tk/test-data/input_alkanes.txt new file mode 100644 index 00000000..50b8bfc4 --- /dev/null +++ b/tools/rcx-tk/test-data/input_alkanes.txt @@ -0,0 +1,10 @@ +Carbon number RT (min) +12 2.8 +13 3.0 +14 3.3 +15 3.7 +16 4.2 +17 4.6 +18 5.0 +19 5.4 +20 5.7 diff --git a/tools/rcx-tk/test-data/input_metadata.tabular b/tools/rcx-tk/test-data/input_metadata.tabular new file mode 100644 index 00000000..3eaa807b --- /dev/null +++ b/tools/rcx-tk/test-data/input_metadata.tabular @@ -0,0 +1,12 @@ +File path File name Type Class ID Batch Analytical order Inject. volume (μL) Included +Z:\000020-Shares\hram\MS_omics\Personal Folders\COUFALIKOVA Katerina\ATHLETE\finalni data zaloha\batch1-20231121-Katerina Coufalikova\RAW_profile\1_instrumental blank_01.raw 1_instrumental blank_01 Standard 3 1 1 6 TRUE +Z:\000020-Shares\hram\MS_omics\Personal Folders\COUFALIKOVA Katerina\ATHLETE\finalni data zaloha\batch1-20231121-Katerina Coufalikova\RAW_profile\4_Alkane mix_04.raw 4_Alkane mix_04 Standard 5 1 4 6 TRUE +Z:\000020-Shares\hram\MS_omics\Personal Folders\COUFALIKOVA Katerina\ATHLETE\finalni data zaloha\batch1-20231121-Katerina Coufalikova\RAW_profile\6_instrumental blank_06.raw 6_instrumental blank_06 Standard 3 1 6 6 TRUE +Z:\000020-Shares\hram\MS_omics\Personal Folders\COUFALIKOVA Katerina\ATHLETE\finalni data zaloha\batch1-20231121-Katerina Coufalikova\RAW_profile\7_procedural blank_07.raw 7_procedural blank_07 Blank 6 1 7 6 TRUE +Z:\000020-Shares\hram\MS_omics\Personal Folders\COUFALIKOVA Katerina\ATHLETE\finalni data zaloha\batch1-20231121-Katerina Coufalikova\RAW_profile\8_QC non-dilute_08.raw 8_QC non-dilute_08 QC 2 1 8 6 TRUE +Z:\000020-Shares\hram\MS_omics\Personal Folders\COUFALIKOVA Katerina\ATHLETE\finalni data zaloha\batch1-20231121-Katerina Coufalikova\RAW_profile\11_QC 16_11.raw 11_QC 16_11 QC 2 1 11 6 TRUE +Z:\000020-Shares\hram\MS_omics\Personal Folders\COUFALIKOVA Katerina\ATHLETE\finalni data zaloha\batch1-20231121-Katerina Coufalikova\RAW_profile\12_QC 8_12.raw 12_QC 8_12 QC 2 1 12 6 TRUE +Z:\000020-Shares\hram\MS_omics\Personal Folders\COUFALIKOVA Katerina\ATHLETE\finalni data zaloha\batch1-20231121-Katerina Coufalikova\RAW_profile\15_QC non-dilute_15.raw 15_QC non-dilute_15 QC 2 1 15 6 TRUE +Z:\000020-Shares\hram\MS_omics\Personal Folders\COUFALIKOVA Katerina\ATHLETE\finalni data zaloha\batch1-20231121-Katerina Coufalikova\RAW_profile\18_QC 4 _18.raw 18_QC 4 _18 QC 2 1 18 6 TRUE +Z:\000020-Shares\hram\MS_omics\Personal Folders\COUFALIKOVA Katerina\ATHLETE\finalni data zaloha\batch1-20231121-Katerina Coufalikova\RAW_profile\19_QC 8_19.raw 19_QC 8_19 QC 2 1 19 6 TRUE +Z:\000020-Shares\hram\MS_omics\Personal Folders\COUFALIKOVA Katerina\ATHLETE\finalni data zaloha\batch1-20231121-Katerina Coufalikova\RAW_profile\29_instrument blank_29.raw 29_instrument blank_29 Standard 3 1 29 6 TRUE diff --git a/tools/rcx-tk/test-data/output_alkanes.tsv b/tools/rcx-tk/test-data/output_alkanes.tsv new file mode 100644 index 00000000..b80db1c0 --- /dev/null +++ b/tools/rcx-tk/test-data/output_alkanes.tsv @@ -0,0 +1,10 @@ +carbon_number rt +12 2.8 +13 3.0 +14 3.3 +15 3.7 +16 4.2 +17 4.6 +18 5.0 +19 5.4 +20 5.7 diff --git a/tools/rcx-tk/test-data/output_metadata.tsv b/tools/rcx-tk/test-data/output_metadata.tsv new file mode 100644 index 00000000..65af11b1 --- /dev/null +++ b/tools/rcx-tk/test-data/output_metadata.tsv @@ -0,0 +1,12 @@ +sampleName sampleType class batch injectionOrder sequenceIdentifier subjectIdentifier localOrder +1_instrumental_blank_01 Standard 3 1 1 1_instrumental blank instrumental blank 1 +4_Alkane_mix_04 Standard 5 1 4 4_Alkane mix Alkane mix 4 +6_instrumental_blank_06 Standard 3 1 6 6_instrumental blank instrumental blank 6 +7_procedural_blank_07 Blank 6 1 7 7_procedural blank procedural blank 7 +8_QC_non-dilute_08 QC 2 1 8 8_QC non-dilute QC non-dilute 8 +11_QC_16_11 QC 2 1 11 11_QC 16 QC 16 11 +12_QC_8_12 QC 2 1 12 12_QC 8 QC 8 12 +15_QC_non-dilute_15 QC 2 1 15 15_QC non-dilute QC non-dilute 15 +18_QC_4__18 QC 2 1 18 18_QC 4 QC 4 18 +19_QC_8_19 QC 2 1 19 19_QC 8 QC 8 19 +29_instrument_blank_29 Standard 3 1 29 29_instrument blank instrument blank 29