Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes
changeset 33:c75cfa968e2a draft
Uploaded
| author | jackcurragh |
|---|---|
| date | Fri, 23 Sep 2022 14:09:06 +0000 |
| parents | cb5a2a3ed8e7 |
| children | d82cc435c5c8 |
| files | get_chrom_sizes/get_chrom_sizes.xml |
| diffstat | 1 files changed, 9 insertions(+), 2 deletions(-) [+] |
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--- a/get_chrom_sizes/get_chrom_sizes.xml Fri Sep 23 14:05:11 2022 +0000 +++ b/get_chrom_sizes/get_chrom_sizes.xml Fri Sep 23 14:09:06 2022 +0000 @@ -8,7 +8,7 @@ ${refGenomeSource.input1_file} none ${output1} #end if --> - #if $refGenomeSource.genomeSource == "builtin": + <!-- #if $refGenomeSource.genomeSource == "builtin": #if ${input2} == "chr": cat ${refGenomeSource.input1_builtin.fields.path} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf "chr" substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1 #else: @@ -20,6 +20,13 @@ #else: cat ${refGenomeSource.input1_file} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1 #end if + #end if --> + + #if $refGenomeSource.genomeSource == "builtin": + cat ${refGenomeSource.input1_builtin.fields.path} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf ${input2} substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1 + #else: + #if ${input2} == "chr": + cat ${refGenomeSource.input1_file} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf ${input2} substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1 #end if </command> @@ -43,7 +50,7 @@ </conditional> <param name="input2" type="select" label="Chromosome Column Prefix (eg. chr)"> <option value="chr">'chr' (required for upload to GWIPS-Viz)</option> - <option value="none" selected='true'>None - do not add a prefix</option> + <option value="" selected='true'>None - do not add a prefix</option> </param> </inputs>