Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

comparison get_chrom_sizes/get_chrom_sizes.xml @ 33:c75cfa968e2a draft

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Uploaded
author jackcurragh
date Fri, 23 Sep 2022 14:09:06 +0000
parents cb5a2a3ed8e7
children d82cc435c5c8
comparison
equal deleted inserted replaced
32:cb5a2a3ed8e7 33:c75cfa968e2a
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
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 -->
24
25 #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
27 #else:
28 #if ${input2} == "chr":
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
23 #end if 30 #end if
24 31
25 </command> 32 </command>
26 <inputs> 33 <inputs>
27 <conditional name="refGenomeSource"> 34 <conditional name="refGenomeSource">
41 <param name="input1_file" type="data" format="fasta" label="FASTA File" /> 48 <param name="input1_file" type="data" format="fasta" label="FASTA File" />
42 </when> 49 </when>
43 </conditional> 50 </conditional>
44 <param name="input2" type="select" label="Chromosome Column Prefix (eg. chr)"> 51 <param name="input2" type="select" label="Chromosome Column Prefix (eg. chr)">
45 <option value="chr">'chr' (required for upload to GWIPS-Viz)</option> 52 <option value="chr">'chr' (required for upload to GWIPS-Viz)</option>
46 <option value="none" selected='true'>None - do not add a prefix</option> 53 <option value="" selected='true'>None - do not add a prefix</option>
47 </param> 54 </param>
48 55
49 </inputs> 56 </inputs>
50 <outputs> 57 <outputs>
51 <data name="output1" format="tabular"/> 58 <data name="output1" format="tabular"/>