Mercurial > repos > devteam > vcf_filter
comparison filter.xml @ 0:da1a6f33b504 draft default tip
Imported from capsule None
| author | devteam |
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| date | Mon, 27 Jan 2014 09:29:09 -0500 |
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| -1:000000000000 | 0:da1a6f33b504 |
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| 1 <tool id="vcf_filter" name="Filter" version="1.0.0"> | |
| 2 <description>a VCF file</description> | |
| 3 <command interpreter="python"> | |
| 4 vcfPytools.py | |
| 5 filter | |
| 6 --in=$input1 | |
| 7 --out=$output1 | |
| 8 --quality=$quality | |
| 9 #for $i in $info_filter: | |
| 10 --info ${i.info} | |
| 11 #end for | |
| 12 $remove_genotypes | |
| 13 $mark_as_pass | |
| 14 </command> | |
| 15 <inputs> | |
| 16 <param name="input1" label="VCF file" type="data" format="vcf" /> | |
| 17 <param name="quality" label="Filter by quality" type="integer" value='' help="Filter out SNPs with qualities lower than selected value" /> | |
| 18 <repeat name="info_filter" title="Filter based on entries in the info string"> | |
| 19 <param name="info" label="Filter" type="text" value='' help='This option takes three values: the info string tag, the cutoff value and whether to filter out those records with less than (lt) or greater than (gt) this value. For example: DP 10 lt ' /> | |
| 20 </repeat> | |
| 21 <param name="remove_genotypes" label="Remove the genotype strings" type="boolean" truevalue="--remove-genotypes" falsevalue="" checked="False" /> | |
| 22 <param name="mark_as_pass" label="Mark all records as having passed filters" type="boolean" truevalue="--mark-as-pass" falsevalue="" checked="False" /> | |
| 23 </inputs> | |
| 24 <tests> | |
| 25 <test> | |
| 26 <param name="input1" value="test.small.vcf" ftype="vcf" /> | |
| 27 <param name="quality" value="9" /> | |
| 28 <param name="info" value="NS 360 gt"/> | |
| 29 <param name="remove_genotypes" value="" /> | |
| 30 <param name="mark_as_pass" value="" /> | |
| 31 <output name="output" file="test_filter_quality_9_NS_360_gt.vcf" lines_diff="6" ftype="vcf" /> | |
| 32 </test> | |
| 33 <test> | |
| 34 <param name="input1" value="test.small.vcf" ftype="vcf" /> | |
| 35 <param name="quality" value="9" /> | |
| 36 <param name="info" value="DP 2000 lt"/> | |
| 37 <param name="remove_genotypes" value="" /> | |
| 38 <param name="mark_as_pass" value="" /> | |
| 39 <output name="output" file="test_filter_quality_9_DP_2000_lt.vcf" lines_diff="6" ftype="vcf" /> | |
| 40 </test> | |
| 41 </tests> | |
| 42 <outputs> | |
| 43 <data format="vcf" name="output1" label="${tool.name} ${on_string}" /> | |
| 44 </outputs> | |
| 45 <help> | |
| 46 | |
| 47 **What it does** | |
| 48 | |
| 49 This tool uses vcfPytools_' filter command | |
| 50 | |
| 51 .. _vcfPytools: https://github.com/AlistairNWard/vcfPytools | |
| 52 | |
| 53 Quality option will check the variant quality for each record and if it is below the defined value, the filter field will be populated with the filter entry Q[value]. | |
| 54 | |
| 55 Any value in the info string can be used for filtering by using the 'Filter by info' option. This option takes three values: the info string tag, the cutoff value and whether to filter out those records with less than (lt) or greater than (gt) this value. For example: | |
| 56 | |
| 57 DP 10 lt | |
| 58 | |
| 59 would filter out all varianta with a depth (DP) less than 10 and the filter field would be populated with DP10. | |
| 60 | |
| 61 This option can be defined as many times as required. | |
| 62 | |
| 63 </help> | |
| 64 </tool> |