Column header issue

[mthang]

@bebatut One of the Galaxy Australia users has spotted a minor issue regarding the format of the column header in the final output table. The column name is presented in the format of the Galaxy filename (i.e dataset_13024425) instead of the filename of interest (i.e mysampleID). Therefore, it it very difficult to develop a workflow with merge_metaphlan_tables wrapper.

We have found that the wrapper can be improved by using the code from the humann_join_tables.xml wrapper which uses the element.identifier to capture the Sample/ID from the input files.

https://github.com/galaxyproject/tools-iuc/blob/6f7d090f3c68336bace91ab1fe4f9c1163d943db/tools/metaphlan/merge_metaphlan_tables.xml#L10

Many thanks

[vmurigneu]

Hi @bebatut, here is an example to illustrate what seems to be missing from the Metaphlan wrapper:

This is the command human_join2 is doing for merge the HUMAN2 tables: the fastq files are renamed to their original names in a tmp folder mkdir tmp_dir && cp '/mnt/user-data-7/013/024/dataset_13024425.dat' 'tmp_dir/UAS010V1.fastq.gz' && cp '/mnt/user-data-7/013/024/dataset_13024428.dat' 'tmp_dir/UAS009V2.fastq.gz' && humann2_join_tables -i 'tmp_dir' -o '/mnt/tmp/job_working_directory/005/950/5950057/outputs/galaxy_dataset_70cd1fc9-97c9-424a-878d-ab67443c3109.dat'

But Metaphlan command line to merge the tables look like this: merge_metaphlan_tables.py '/mnt/user-data-7/013/169/dataset_13169341.dat' '/mnt/user-data-7/013/169/dataset_13169344.dat' '/mnt/user-data-7/013/169/dataset_13169347.dat' > '/mnt/tmp/job_working_directory/005/950/5950246/outputs/galaxy_dataset_d252cc6e-a7e6-407b-b960-38192ee2a5d7.dat'

Thank you for your help, Valentine

[TomHarrop]

@mthang is this what you mean?

https://github.com/galaxyproject/tools-iuc/pull/5700