From 0a18c208fd40a8a4411593d4c745b16cd87c58df Mon Sep 17 00:00:00 2001 From: KristinaGomoryova Date: Thu, 1 Aug 2024 13:29:26 +0200 Subject: [PATCH 1/7] initial commit of the rcx-tk galaxy wrapper --- tools/rcx-tk/.shed.yml | 9 +++ tools/rcx-tk/rcx-tk.xml | 70 +++++++++++++++++++ tools/rcx-tk/test-data/input_alkanes.txt | 10 +++ tools/rcx-tk/test-data/input_metadata.tabular | 12 ++++ tools/rcx-tk/test-data/output_alkanes.tsv | 10 +++ tools/rcx-tk/test-data/output_metadata.tsv | 12 ++++ 6 files changed, 123 insertions(+) create mode 100644 tools/rcx-tk/.shed.yml create mode 100644 tools/rcx-tk/rcx-tk.xml create mode 100644 tools/rcx-tk/test-data/input_alkanes.txt create mode 100644 tools/rcx-tk/test-data/input_metadata.tabular create mode 100644 tools/rcx-tk/test-data/output_alkanes.tsv create mode 100644 tools/rcx-tk/test-data/output_metadata.tsv diff --git a/tools/rcx-tk/.shed.yml b/tools/rcx-tk/.shed.yml new file mode 100644 index 00000000..ebfc4391 --- /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..04842b6d --- /dev/null +++ b/tools/rcx-tk/rcx-tk.xml @@ -0,0 +1,70 @@ + + + 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..e29ec412 --- /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..e8813e0d --- /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 From 09b8ee5661b3b4ad91b9e85ed3690e7c044e321b Mon Sep 17 00:00:00 2001 From: KristinaGomoryova Date: Thu, 1 Aug 2024 13:41:43 +0200 Subject: [PATCH 2/7] rcx_tk instead of rcx-tk --- tools/rcx-tk/.shed.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/rcx-tk/.shed.yml b/tools/rcx-tk/.shed.yml index ebfc4391..3f7829f2 100644 --- a/tools/rcx-tk/.shed.yml +++ b/tools/rcx-tk/.shed.yml @@ -1,4 +1,4 @@ -name: rcx-tk +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" From c90d5688f42fb23c9850b2a9655678960dc08750 Mon Sep 17 00:00:00 2001 From: KristinaGomoryova Date: Thu, 1 Aug 2024 13:55:00 +0200 Subject: [PATCH 3/7] convert to unix line endings --- tools/rcx-tk/test-data/input_alkanes.txt | 20 ++++++++-------- tools/rcx-tk/test-data/input_metadata.tabular | 24 +++++++++---------- 2 files changed, 22 insertions(+), 22 deletions(-) diff --git a/tools/rcx-tk/test-data/input_alkanes.txt b/tools/rcx-tk/test-data/input_alkanes.txt index e29ec412..50b8bfc4 100644 --- a/tools/rcx-tk/test-data/input_alkanes.txt +++ b/tools/rcx-tk/test-data/input_alkanes.txt @@ -1,10 +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 +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 index e8813e0d..3eaa807b 100644 --- a/tools/rcx-tk/test-data/input_metadata.tabular +++ b/tools/rcx-tk/test-data/input_metadata.tabular @@ -1,12 +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 +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 From e2ab3daf020fcd28a031fa8920841945b9de4e25 Mon Sep 17 00:00:00 2001 From: hechth Date: Thu, 1 Aug 2024 14:08:44 +0200 Subject: [PATCH 4/7] changed input file copying to local directory --- tools/rcx-tk/rcx-tk.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/rcx-tk/rcx-tk.xml b/tools/rcx-tk/rcx-tk.xml index 04842b6d..9054c321 100644 --- a/tools/rcx-tk/rcx-tk.xml +++ b/tools/rcx-tk/rcx-tk.xml @@ -30,9 +30,9 @@ Date: Thu, 1 Aug 2024 14:18:19 +0200 Subject: [PATCH 5/7] organization added --- tools/rcx-tk/rcx-tk.xml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tools/rcx-tk/rcx-tk.xml b/tools/rcx-tk/rcx-tk.xml index 9054c321..93b5a877 100644 --- a/tools/rcx-tk/rcx-tk.xml +++ b/tools/rcx-tk/rcx-tk.xml @@ -27,6 +27,10 @@ familyName="Hecht" url="https://github.com/hechth" identifier="0000-0001-6744-996X" /> + Date: Thu, 1 Aug 2024 14:29:47 +0200 Subject: [PATCH 6/7] parameters help added --- tools/rcx-tk/rcx-tk.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/rcx-tk/rcx-tk.xml b/tools/rcx-tk/rcx-tk.xml index 93b5a877..6ec15cb2 100644 --- a/tools/rcx-tk/rcx-tk.xml +++ b/tools/rcx-tk/rcx-tk.xml @@ -42,8 +42,8 @@ python3 -m rcx_tk --method ${method} ${input_file_new} 'output.tsv' ]]> - - + + From 0318288c6ccf1f77ff4cf51544b95816167a1c22 Mon Sep 17 00:00:00 2001 From: KristinaGomoryova Date: Thu, 1 Aug 2024 14:30:56 +0200 Subject: [PATCH 7/7] typo corrected --- tools/rcx-tk/rcx-tk.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/rcx-tk/rcx-tk.xml b/tools/rcx-tk/rcx-tk.xml index 6ec15cb2..40e2c55c 100644 --- a/tools/rcx-tk/rcx-tk.xml +++ b/tools/rcx-tk/rcx-tk.xml @@ -42,7 +42,7 @@ python3 -m rcx_tk --method ${method} ${input_file_new} 'output.tsv' ]]> - +