Mercurial > repos > devteam > divide_pg_snp
diff dividePgSnpAlleles.xml @ 0:de839553d2a2
Uploaded tool tarball.
author | devteam |
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date | Wed, 25 Sep 2013 10:26:17 -0400 |
parents | |
children | f74fdfc17143 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dividePgSnpAlleles.xml Wed Sep 25 10:26:17 2013 -0400 @@ -0,0 +1,76 @@ +<tool id="dividePgSnp" version="1.0.0" name="Separate pgSnp alleles" hidden="false"> + <description>into columns</description> + <command interpreter="perl"> + #if $refcol.ref == "yes" #dividePgSnpAlleles.pl -ref=$refcol.ref_column $input1 > $out_file1 + #else #dividePgSnpAlleles.pl $input1 > $out_file1 + #end if + </command> + <inputs> + <param format="interval" version="1.0.0" name="input1" type="data" label="pgSnp dataset" /> + <conditional version="1.0.0" name="refcol"> + <param version="1.0.0" name="ref" type="select" label="Dataset has a column with the reference allele:"> + <option value="yes">yes</option> + <option value="no" selected="true">no</option> + </param> + <when value="yes"> + <param version="1.0.0" name="ref_column" type="data_column" data_ref="input1" label="Column with reference allele" /> + </when> + <when value="no"> <!-- do nothing --> + </when> + </conditional> + </inputs> + <outputs> + <data format="interval" version="1.0.0" name="out_file1" /> + </outputs> + <tests> + <test> + <param name='input1' value='dividePgSnp_input.pgSnp' ftype='interval' /> + <param name='ref' value='no' /> + <output version="1.0.0" name="output" file="dividePgSnp_output.txt" /> + </test> + </tests> + + <help> +**Dataset formats** + +The input dataset is of Galaxy datatype interval_ with the columns specified +for pgSnp_. +Any additional columns beyond the pgSnp defined columns will be appended to +the output. +The output dataset is in interval_ format. (`Dataset missing?`_) + +.. _interval: ./static/formatHelp.html#interval +.. _Dataset missing?: ./static/formatHelp.html +.. _pgSnp: ./static/formatHelp.html#pgSnp + +**What it does** + +This separates the alleles from a pgSnp dataset into separate columns, +as well as the frequencies and scores that go with the alleles. It will skip +any positions with more than 2 alleles. If only a single allele is given then "N" +will be used for the second, with a frequency and score of zero. Or, if a +column with reference alleles is provided, +the value in that column will be used in place of the "N" for single alleles. + +----- + +**Examples** + +- input pgSnp file:: + + chr1 256 257 A/C 2 3,4 10,20 + chr1 56100 56101 A 1 5 30 + chr1 77052 77053 A/G 2 6,7 40,50 + chr1 110904 110905 A 1 8 60 + etc. + +- output:: + + chr1 256 257 A 3 10 C 4 20 + chr1 56100 56101 A 5 30 N 0 0 + chr1 77052 77053 A 6 40 G 7 50 + chr1 110904 110905 A 8 60 N 0 0 + etc. + +</help> +</tool>