Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

comparison get_chrom_sizes/get_chrom_sizes.xml @ 32:cb5a2a3ed8e7 draft

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author jackcurragh
date Fri, 23 Sep 2022 14:05:11 +0000
parents 75df50cfe7a9
children c75cfa968e2a
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31:75df50cfe7a9 32:cb5a2a3ed8e7
1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.6"> 1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.7">
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 if ${input2} == "chr": 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 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: 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 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 end if 16 #end if
17 #else: 17 #else:
18 if ${input2} == "chr": 18 #if ${input2} == "chr":
19 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 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
20 else: 20 #else:
21 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 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
22 end if 22 #end if
23 #end if 23 #end if
24 24
25 </command> 25 </command>
26 <inputs> 26 <inputs>
27 <conditional name="refGenomeSource"> 27 <conditional name="refGenomeSource">