Mercurial > repos > bimib > cobraxy
changeset 82:226bee471503 draft
Uploaded
| author | luca_milaz |
|---|---|
| date | Sun, 13 Oct 2024 11:03:02 +0000 |
| parents | a30013ece710 |
| children | bfb17674d13b |
| files | COBRAxy/ras_to_bounds.xml |
| diffstat | 1 files changed, 8 insertions(+), 2 deletions(-) [+] |
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--- a/COBRAxy/ras_to_bounds.xml Sun Oct 13 10:57:49 2024 +0000 +++ b/COBRAxy/ras_to_bounds.xml Sun Oct 13 11:03:02 2024 +0000 @@ -29,6 +29,11 @@ --ras_selector $cond_ras.ras_choice #if $cond_ras.ras_choice == "True" --input_ras $cond_ras.input_ras + #set $names = "" + #for $input_temp in $cond_ras.input_ras: + #set $names = $names + $input_temp.element_identifier + "," + #end for + --names $names #end if --out_log $log ]]> @@ -85,7 +90,7 @@ - RAS matrix: tab-separated RAS file as returned by RAS generator. Multiple RAS files can be uploaded too (e.g. one RAS matrix for normal cells and one for cancer cells). Note that if multiple RAs matrices are uploaded, the bounds are normalzed across all cells. - Medium: tab-separated file containing lower and upper-bounds of medium reactions. -Example of custum growth medium fileeeee: +Example of custum growth medium file: +------------+----------------+----------------+ @@ -98,7 +103,8 @@ Example for multiple RAS matrices: - cancer.csv and normal.csv generated by RAS generator tool (the two class names are 'cancer' and 'normal'). - - This tool returns one unique collection of bounds files for both cancer and normal cells (normalization is performed across all cells). ++ +− - This tool returns one unique collection of bounds files for both cancer and normal cells (normalization is performed across all cells). - The association cell-class is reported in the 'cell_class' file that is useful to perform flux enrichment analysis based on class partenrship. Output: