Mercurial > repos > miller-lab > genome_diversity
view filter_gd_snp.xml @ 17:a3af29edcce2
Uploaded Miller Lab Devshed version a51c894f5bed
author | miller-lab |
---|---|
date | Fri, 28 Sep 2012 11:57:18 -0400 |
parents | fdb4240fb565 |
children | f04f40a36cc8 |
line wrap: on
line source
<tool id="gd_filter_gd_snp" name="Filter SNPs" version="1.0.0"> <description>: Discard some SNPs based on coverage or quality</description> <command interpreter="python"> modify_snp_table.py "$input" "$p1_input" "$output" "$lo_coverage" "$hi_coverage" "$low_ind_cov" "$lo_quality" #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) #set $arg = '%s:%s' % ($individual_col, $individual) "$arg" #end for </command> <inputs> <param name="input" type="data" format="gd_snp" label="SNP dataset" /> <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" /> <param name="lo_coverage" type="integer" min="0" value="0" label="Lower bound on total coverage" /> <param name="hi_coverage" type="integer" min="0" value="1000" label="Upper bound on total coverage" /> <param name="low_ind_cov" type="integer" min="0" value="0" label="Lower bound on individual coverage" /> <param name="lo_quality" type="integer" min="0" value="0" label="Lower bound on individual quality values" /> </inputs> <outputs> <data name="output" format="gd_snp" metadata_source="input" /> </outputs> <tests> <test> <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> <param name="choice" value="1" /> <param name="lo_coverage" value="0" /> <param name="hi_coverage" value="1000" /> <param name="low_ind_cov" value="3" /> <param name="lo_quality" value="30" /> <output name="output" file="test_out/modify_snp_table/modify.gd_snp" /> </test> </tests> <help> **Dataset formats** The input datasets are in gd_snp_ and gd_indivs_ formats. The output dataset is in gd_snp_ format. (`Dataset missing?`_) .. _gd_snp: ./static/formatHelp.html#gd_snp .. _gd_indivs: ./static/formatHelp.html#gd_indivs .. _Dataset missing?: ./static/formatHelp.html ----- **What it does** The user specifies that some of the individuals in a gd_snp dataset form a "population", by supplying a list that has been previously created using the Specify Individuals tool. SNPs are then discarded if their total coverage for the population is too low or too high, or if their coverage or quality score for any individual in the population is too low. ----- **Example** - input gd_snp:: Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0 Contig48_chr1_10150253_10151311 11 A G 94.3 chr1 10150264 A 1 0 2 30 1 0 2 30 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 Y 22 +99. 0 Contig20_chr1_21313469_21313570 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0 etc. - input individuals:: 9 PB1 13 PB2 17 PB3 - output when the lower bound on individual coverage is "3":: Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0 Contig20_chr1_21313469_21313570 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0 etc. </help> </tool>