Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

comparison get_chrom_sizes/get_chrom_sizes.xml @ 34:d82cc435c5c8 draft

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author jackcurragh
date Fri, 23 Sep 2022 14:14:04 +0000
parents c75cfa968e2a
children 6932d7b12b41
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33:c75cfa968e2a 34:d82cc435c5c8
1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.7"> 1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8">
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}
5 #if $refGenomeSource.genomeSource == "builtin":
6 none ${refGenomeSource.input1_builtin.fields.path} ${output1}
7 #else:
8 ${refGenomeSource.input1_file} none ${output1}
9 #end if -->
10
11 <!-- #if $refGenomeSource.genomeSource == "builtin":
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 #end if
17 #else:
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
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
22 #end if
23 #end if -->
24 4
25 #if $refGenomeSource.genomeSource == "builtin": 5 #if $refGenomeSource.genomeSource == "builtin":
26 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 6 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
27 #else: 7 #else:
28 #if ${input2} == "chr": 8 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
29 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
30 #end if 9 #end if
31 10
32 </command> 11 </command>
33 <inputs> 12 <inputs>
34 <conditional name="refGenomeSource"> 13 <conditional name="refGenomeSource">