Mercurial > repos > greg > affy_ids_for_genotyping
comparison affy_ids_for_genotyping.xml @ 0:d4c49015dac0 draft
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author | greg |
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date | Thu, 15 Aug 2019 09:32:13 -0400 |
parents | |
children | 326bee593418 |
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1 <tool id="affy_ids_for_genotyping" name="Extract Affymetrix ids for genotyping" version="1.0.0"> | |
2 <description>from VCF data</description> | |
3 <command detect_errors="exit_code"><![CDATA[ | |
4 grep "#CHROM" '$input_vcf' > test.head && | |
5 tr '\t' '\n' < test.head > samples.txt && | |
6 sed -i 1,9d samples.txt && | |
7 awk -F'\t' -v OFS='\t' 'NR==0 {print ; next}{print (NR),$0}' samples.txt > '$output' | |
8 ]]></command> | |
9 <inputs> | |
10 <param name="input_vcf" type="data" format="vcf" label="VCF file"/> | |
11 </inputs> | |
12 <outputs> | |
13 <data name="output" format="tabular"/> | |
14 </outputs> | |
15 <tests> | |
16 <test> | |
17 <param name="input_vcf" value="input.vcf" ftype="vcf"/> | |
18 <output name="output" file="output.tabular" ftype="tabular"/> | |
19 </test> | |
20 </tests> | |
21 <help> | |
22 **What it does** | |
23 | |
24 Extracts information from a VCF file that contains Affymetrix identifiers and produces a file that contains | |
25 a subset of the identifiers combined with additional data to generate the genotype population information | |
26 for use as input to the Corals Multilocus Genotype tool. This tool must be able to access the corals (stag) | |
27 database. | |
28 </help> | |
29 <citations> | |
30 <citation type="bibtex"> | |
31 @misc{None, | |
32 journal = {None}, | |
33 author = {Baums I}, | |
34 title = {Manuscript in preparation}, | |
35 year = {None}, | |
36 url = {http://baumslab.org} | |
37 </citation> | |
38 </citations> | |
39 </tool> |