Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

comparison get_chrom_sizes/get_chrom_sizes.xml @ 28:c81aa97acf65 draft

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author jackcurragh
date Tue, 30 Aug 2022 10:54:24 +0000
parents a6b6e48756f9
children 190fa66855a8
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27:a6b6e48756f9 28:c81aa97acf65
1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.3"> 1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.4">
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 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: 13 #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 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
16 #end if 15 #end if
17 </command> 16 </command>
18 <inputs> 17 <inputs>