Mercurial > repos > miller-lab > genome_diversity
annotate modify_snp_table.xml @ 9:22fe0154fa54
added support for heterochromatic regions
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Tue, 10 Jul 2012 11:41:22 -0400 |
| parents | e29f4d801bb0 |
| children | 9b92372de9f6 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gd_modify_snp_table" name="Modify" version="1.0.0"> |
| 2 <description>a SNP table</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 modify_snp_table.py "$input" "$p1_input" "$output" | |
| 6 #if $limit_coverage.choice == "0" | |
| 7 "-1" "-1" "-1" "-1" | |
| 8 #else | |
| 9 "${limit_coverage.lo_coverage}" "${limit_coverage.hi_coverage}" "${limit_coverage.low_ind_cov}" "${limit_coverage.lo_quality}" | |
| 10 #end if | |
| 11 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) | |
| 12 #set $arg = '%s:%s' % ($individual_col, $individual) | |
| 13 "$arg" | |
| 14 #end for | |
| 15 </command> | |
| 16 | |
| 17 <inputs> | |
|
7
e29f4d801bb0
change wsf -> snp; wpf -> sap
Richard Burhans <burhans@bx.psu.edu>
parents:
0
diff
changeset
|
18 <param name="input" type="data" format="snp" label="SNP table" /> |
| 0 | 19 <param name="p1_input" type="data" format="ind" label="Population individuals" /> |
| 20 <conditional name="limit_coverage"> | |
| 21 <param name="choice" type="select" format="integer" label="Option"> | |
| 22 <option value="0" selected="true">add columns to the SNP table</option> | |
| 23 <option value="1">discard some SNPs</option> | |
| 24 </param> | |
| 25 <when value="0" /> | |
| 26 <when value="1"> | |
| 27 <param name="lo_coverage" type="integer" min="0" value="0" label="Lower bound on total coverage" /> | |
| 28 <param name="hi_coverage" type="integer" min="0" value="1000" label="Upper bound on total coverage" /> | |
| 29 <param name="low_ind_cov" type="integer" min="0" value="0" label="Lower bound on individual coverage" /> | |
| 30 <param name="lo_quality" type="integer" min="0" value="0" label="Lower bound on individual quality values" /> | |
| 31 </when> | |
| 32 </conditional> | |
| 33 </inputs> | |
| 34 | |
| 35 <outputs> | |
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7
e29f4d801bb0
change wsf -> snp; wpf -> sap
Richard Burhans <burhans@bx.psu.edu>
parents:
0
diff
changeset
|
36 <data name="output" format="snp" metadata_source="input" /> |
| 0 | 37 </outputs> |
| 38 | |
| 39 <tests> | |
| 40 <test> | |
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7
e29f4d801bb0
change wsf -> snp; wpf -> sap
Richard Burhans <burhans@bx.psu.edu>
parents:
0
diff
changeset
|
41 <param name="input" value="test_in/sample.snp" ftype="snp" /> |
| 0 | 42 <param name="p1_input" value="test_in/a.ind" ftype="ind" /> |
| 43 <param name="choice" value="1" /> | |
| 44 <param name="lo_coverage" value="0" /> | |
| 45 <param name="hi_coverage" value="1000" /> | |
| 46 <param name="low_ind_cov" value="3" /> | |
| 47 <param name="lo_quality" value="30" /> | |
|
7
e29f4d801bb0
change wsf -> snp; wpf -> sap
Richard Burhans <burhans@bx.psu.edu>
parents:
0
diff
changeset
|
48 <output name="output" file="test_out/modify_snp_table/modify.snp" /> |
| 0 | 49 </test> |
| 50 </tests> | |
| 51 | |
| 52 <help> | |
| 53 **What it does** | |
| 54 | |
| 55 The user specifies that some of the individuals in the selected SNP table are | |
| 56 form a "population" that has been previously defined using the Galaxy tool to | |
| 57 select individuals from a SNP table. One option is for the program to append | |
| 58 four columns to the table, giving the total counts for the two alleles, the | |
| 59 "genotype" for the population and the maximum quality value, taken over all | |
| 60 individuals in the population. If all defined genotypes in the population | |
| 61 are 2 (agree with the reference), the population's genotype is 2; similarly | |
| 62 for 0; otherwise the genotype is 1 (unless all individuals have undefined | |
| 63 genotype, in which case it is -1. The other option is to remove rows from | |
| 64 the table for which the total coverage for the population is either too low | |
| 65 or too high, and/or if the individual coverage or quality value is too low. | |
| 66 </help> | |
| 67 </tool> |