Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes
comparison get_chrom_sizes/get_chrom_sizes.xml @ 29:190fa66855a8 draft
Uploaded
author | jackcurragh |
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date | Fri, 23 Sep 2022 13:55:45 +0000 |
parents | c81aa97acf65 |
children | c1f79fd2cecd |
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28:c81aa97acf65 | 29:190fa66855a8 |
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1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.4"> | 1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.5"> |
2 <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description> | 2 <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description> |
3 <command> | 3 <command> |
4 <!-- python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} ${input2} | 4 <!-- python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} ${input2} |
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 | 10 |
11 #if $refGenomeSource.genomeSource == "builtin": | 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 | 12 if ${input2} == "chr": |
13 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 | |
14 else: | |
15 cat ${refGenomeSource.input1_builtin.fields.path} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1 | |
16 #else: | |
17 if ${input2} == "chr": | |
18 cat ${refGenomeSource.input1_file} | 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 | |
19 else: | |
20 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 | |
21 #end if | |
22 | |
23 | |
24 | |
25 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 #else: | 26 #else: |
14 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 | 27 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 |
15 #end if | 28 #end if |
16 </command> | 29 </command> |
17 <inputs> | 30 <inputs> |
33 </when> | 46 </when> |
34 </conditional> | 47 </conditional> |
35 <param name="input2" type="select" label="Chromosome Column Prefix (eg. chr)"> | 48 <param name="input2" type="select" label="Chromosome Column Prefix (eg. chr)"> |
36 <option value="chr">'chr' (required for upload to GWIPS-Viz)</option> | 49 <option value="chr">'chr' (required for upload to GWIPS-Viz)</option> |
37 <option value="none" selected='true'>None - do not add a prefix</option> | 50 <option value="none" selected='true'>None - do not add a prefix</option> |
38 <option value="manual">Specify you own</option> | |
39 </param> | 51 </param> |
40 | 52 |
41 </inputs> | 53 </inputs> |
42 <outputs> | 54 <outputs> |
43 <data name="output1" format="tabular"/> | 55 <data name="output1" format="tabular"/> |