Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes
comparison get_chrom_sizes/get_chrom_sizes.xml @ 27:a6b6e48756f9 draft
Uploaded
| author | jackcurragh |
|---|---|
| date | Tue, 30 Aug 2022 10:12:12 +0000 |
| parents | 185133c56545 |
| children | c81aa97acf65 |
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| 26:185133c56545 | 27:a6b6e48756f9 |
|---|---|
| 5 #if $refGenomeSource.genomeSource == "builtin": | 5 #if $refGenomeSource.genomeSource == "builtin": |
| 6 none ${refGenomeSource.input1_builtin.fields.path} ${output1} | 6 none ${refGenomeSource.input1_builtin.fields.path} ${output1} |
| 7 #else: | 7 #else: |
| 8 ${refGenomeSource.input1_file} none ${output1} | 8 ${refGenomeSource.input1_file} none ${output1} |
| 9 #end if | 9 #end if |
| 10 | |
| 11 #if $refGenomeSource.genomeSource == "builtin": | |
| 12 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 | |
| 13 none ${refGenomeSource.input1_builtin.fields.path} ${output1} | |
| 14 #else: | |
| 15 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 | |
| 16 #end if | |
| 10 </command> | 17 </command> |
| 11 <inputs> | 18 <inputs> |
| 12 <conditional name="refGenomeSource"> | 19 <conditional name="refGenomeSource"> |
| 13 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?"> | 20 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?"> |
| 14 <option value="builtin">Use a built-in FASTA</option> | 21 <option value="builtin">Use a built-in FASTA</option> |