Mercurial > repos > ebi-gxa > retrieve_scxa
changeset 1:540cc98d4587 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 3fc448754d6720855f781caa7938e33d3961b092"
| author | ebi-gxa |
|---|---|
| date | Thu, 16 Apr 2020 08:50:10 +0000 |
| parents | d3d48791d81a |
| children | d4755a95c52d |
| files | retrieve-scxa.xml |
| diffstat | 1 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- a/retrieve-scxa.xml Wed Mar 13 19:08:27 2019 -0400 +++ b/retrieve-scxa.xml Thu Apr 16 08:50:10 2020 +0000 @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="retrieve_scxa" name="EBI SCXA Data Retrieval" version="v0.0.1+galaxy1"> +<tool id="retrieve_scxa" name="EBI SCXA Data Retrieval" version="v0.0.2+galaxy2"> <description>Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA)</description> <requirements> - <requirement type="package" version="1.18">gnu-wget</requirement> + <requirement type="package" version="1.20.1">wget</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @@ -19,8 +19,8 @@ wget -O ${matrix_mtx} 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.mtx'; wget -qO - 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.mtx_cols' | cut -f2 > ${barcode_tsv}; -wget -qO - 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.mtx_rows' - | awk '{OFS="\t"; print \$2,\$2}' > ${genes_tsv}; +wget -qO - 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.decorated.mtx_rows' | + awk -F'\t' '{ if (length($2) == 0) { print $1"\t"$1 } else { print $0 } }' > ${genes_tsv}; #end if @@ -88,6 +88,7 @@ already normalized/scaled. You should keep this in mind when using this data on methods that will try to normalise data as part of their procedure. Due to technical particularities in the current Atlas SC pipeline, TPMs available here are not filtered. + **Note: droplet databases won't have TPM data** Outputs will be: @@ -113,5 +114,6 @@ ]]></help> <citations> <citation type="doi">10.1093/nar/gkv1045</citation> + <citation type="doi">10.1101/2020.04.08.032698</citation> </citations> </tool>