Merge pull request RECETOX#563 from KristinaGomoryova/rcx-tk_galaxy

Initial commit of the rcx-tk galaxy wrapper
zargham-ahmad · Aug 1, 2024 · 11666fa · 11666fa
2 parents b88eaca + 0318288
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diff --git a/tools/rcx-tk/.shed.yml 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
diff --git a/tools/rcx-tk/rcx-tk.xml b/tools/rcx-tk/rcx-tk.xml
@@ -0,0 +1,74 @@
+<tool id="rcx-tk" name="rcx-tk" version="0.1.0+galaxy0" python_template_version="3.5" profile="23.05">
+    <edam_topics>
+        <edam_topic>topic_3172</edam_topic>
+        <edam_topic>topic_0091</edam_topic>
+        <edam_topic>topic_3520</edam_topic>       
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_0336</edam_operation>
+        <edam_operation>operation_3695</edam_operation> 
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="0.1.0">rcx-tk</requirement>
+    </requirements>
+    <creator>
+        <person
+                givenName="Zargham"
+                familyName="Ahmad"
+                url="https://github.com/zargham-ahmad"
+                identifier="0000-0000-0000-0000"/>
+        <person
+                givenName="Kristina"
+                familyName="Gomoryova"
+                url="https://github.com/KristinaGomoryova"
+                identifier="0000-0003-4407-3917" />
+        <person
+                givenName="Helge"
+                familyName="Hecht"
+                url="https://github.com/hechth"
+                identifier="0000-0001-6744-996X" />
+        <organization 
+                url="https://www.recetox.muni.cz/"
+                email="[email protected]"
+                name="RECETOX MUNI" />  
+    </creator>
+    <command><![CDATA[
+    #if $input_file.ext == "tabular"
+        #set $input_file_new = 'input.tsv'
+    #else
+        #set $input_file_new = 'input.' + str($input_file.ext)
+    #end if
+       cp ${input_file} ${input_file_new} &&
+       python3 -m rcx_tk --method ${method} ${input_file_new} 'output.tsv' 
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="csv,tabular,tsv,xls,xlsx,txt" label="Input data" help="Input data"/>
+        <param name="method" type="select" label="Method" help="Which data is processed: metadata or alkane file.">
+            <option value="metadata" selected="true">metadata</option>
+            <option value="alkanes">alkanes</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="tabular" from_work_dir = "output.tsv" label="Processed data"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="input_metadata.tabular"/>
+            <param name="method" value="metadata"/>
+            <output name="output_file" file="output_metadata.tsv"/>
+        </test>
+         <test>
+            <param name="input_file" value="input_alkanes.txt"/>
+            <param name="method" value="alkanes"/>
+            <output name="output_file" file="output_alkanes.tsv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    rcx-tk is a tool to process a metadata and/or alkane files. The main steps are columns rearrangement, validation of the file names, and derivation of new columns, such as sampleName, sequenceIdentifier, sampleIdentifier and localOrder. 
+
+    On the input, a metadata or alkane file in any tabular format is expected. On the output, a tsv file is provided.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.5281/zenodo.4471245</citation>
+    </citations>
+</tool>
diff --git a/tools/rcx-tk/test-data/input_alkanes.txt 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
@@ -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
@@ -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
@@ -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