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Add the codingSnps tool.

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Greg Von Kuster
2010-03-23 13:53:21 -04:00
parent b88fc51fa2
commit f129f97f27
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tools/evolution/codingSnps.xml
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<tool id="codingSnps" name="Amino-acid changes">
<description>caused by a set of SNPs</description>
<command interpreter="perl">
codingSnps.pl $input1 $input2 ${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 $out_file1
</command>
<inputs>
<param format="interval" name="input1" type="data" label="SNPs"/>
<param format="interval" name="input2" type="data" label="genes"/>
<param name="col1" label="Column with SNPs" type="data_column" data_ref="input1" />
</inputs>
<outputs>
<data format="input" name="out_file1" />
</outputs>
<code file="codingSnps_filter.py"></code>
<requirements>
<requirement type="binary">twoBitToFa</requirement>
</requirements>
<tests>
<test>
<param name="input1" value="codingSnps_input1.interval" dbkey="hg18" />
<param name="input2" value="codingSnps_input2.bed" dbkey="hg18" />
<param name="col1" value="6" />
<output name="output" file="codingSnps_output.interval" />
</test>
</tests>
<help>
This tool identifies which SNPs create amino-acid changes in the specified coding regions.
**Example**
- first input file, with SNPs::
chr22 14440426 14440427 C/T
chr22 14494851 14494852 A/G
chr22 14494911 14494912 A/T
chr22 14550435 14550436 A/G
chr22 14611956 14611957 G/T
chr22 14612076 14612077 A/G
chr22 14668537 14668538 C
chr22 14668703 14668704 A/T
chr22 14668775 14668776 G
chr22 14680074 14680075 A/T
etc.
alternatively indicating polymorphisms using ambiguous-nucleotide symbols:
chr22 14440426 14440427 Y
chr22 14494851 14494852 R
chr22 14494911 14494912 W
chr22 14550435 14550436 R
chr22 14611956 14611957 K
chr22 14612076 14612077 R
chr22 14668537 14668538 C
chr22 14668703 14668704 W
chr22 14668775 14668776 G
chr22 14680074 14680075 W
etc.
- second input file, with UCSC annotations for human genes::
chr22 14504263 14572999 uc002zkr.2 0 - 14504263 14504263 0 5 710,91,136,138,94, 0,38133,62547,62901,68642,
chr22 14527995 14572999 uc010gqo.1 0 - 14527995 14527995 0 4 3826,91,136,94, 0,14401,38815,44910,
chr22 14542065 14552264 uc002zkt.2 0 + 14542065 14542065 0 3 323,88,313, 0,2416,9886,
chr22 14559619 14561004 uc002zku.2 0 - 14559619 14559619 0 1 1385, 0,
chr22 14567164 14572999 uc002zkv.2 0 - 14567164 14567164 0 5 138,112,115,111,94, 0,1867,2099,3516,5741,
chr22 14620243 14620281 uc002zkw.1 0 - 14620243 14620243 0 1 38, 0,
chr22 14620300 14620339 uc002zkx.1 0 - 14620300 14620300 0 1 39, 0,
chr22 14621086 14621125 uc002zky.1 0 + 14621086 14621086 0 1 39, 0,
chr22 14622000 14622030 uc002zkz.1 0 - 14622000 14622000 0 1 30, 0,
chr22 14623380 14623414 uc002zla.1 0 - 14623380 14623380 0 1 34, 0,
etc.
- output file, showing non-synonymous substitutions in coding regions::
chr22 15452482 15452483 G uc002zlp.1 Trp:Arg 320 A
chr22 15644564 15644565 T uc002zlv.1 His:Asn 442 G
chr22 15645123 15645124 C uc002zlv.1 Phe:Leu 255 A
chr22 15645193 15645194 A/G uc002zlv.1 Pro:Leu/Pro 232 G
chr22 15660821 15660822 A/G uc002zlv.1 Thr:Met/Thr 143 G
chr22 15969208 15969209 C/T uc002zly.1 Ala:Ala/Val 367 C
chr22 15969208 15969209 C/T uc010gqt.1 Ala:Ala/Val 315 C
chr22 15999075 15999076 C/G uc002zmd.1 Arg:Arg/Ser 180 C
chr22 15999075 15999076 C/G uc002zme.1 Arg:Arg/Ser 161 C
chr22 15999075 15999076 C/G uc002zmf.1 Arg:Arg/Ser 369 C
etc.
</help>
</tool>