--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/evolution/codingSnps.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,139 @@
+<tool id="hgv_codingSnps" name="aaChanges" version="1.0.0">
+  <description>amino-acid changes caused by a set of SNPs</description>
+
+  <command interpreter="perl">
+    codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${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="SNP dataset">
+      <validator type="dataset_metadata_in_file" filename="codingSnps.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are not currently available for the specified build." split="\t" />
+    </param>
+    <param name="col1" type="data_column" data_ref="input1" label="Column with SNPs" />
+    <param format="interval" name="input2" type="data" label="Gene dataset">
+      <validator type="dataset_metadata_in_file" filename="codingSnps.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are not currently available for the specified build." split="\t" />
+    </param>
+  </inputs>
+
+  <outputs>
+    <data format="tabular" name="out_file1" />
+  </outputs>
+
+  <code file="codingSnps_filter.py"></code>
+
+  <requirements>
+    <requirement type="binary">cat</requirement>
+    <requirement type="binary">sort</requirement>
+    <requirement type="package">ucsc_tools</requirement>
+  </requirements>
+
+  <tests>
+    <test>
+      <param name="input1" ftype="interval" value="codingSnps_input1.interval" dbkey="hg18" />
+      <param name="col1" value="6" />
+      <param name="input2" ftype="interval" value="codingSnps_inputGenes1.bed" dbkey="hg18" />
+      <output name="output" file="codingSnps_output1.interval" />
+    </test>
+    <test>
+      <param name="input1" ftype="interval" value="codingSnps_input2.interval" dbkey="hg18" />
+      <param name="input2" ftype="interval" value="codingSnps_inputGenes2.bed" dbkey="hg18" />
+      <param name="col1" value="4" />
+      <output name="output" file="codingSnps_output2.interval" />
+    </test>
+  </tests>
+
+  <help>
+.. class:: infomark
+
+The build must be defined for the input files and must be the same for both files.
+Use the pencil icon to add the build to the files if necessary.
+
+-----
+
+**Dataset formats**
+
+The SNP dataset is in interval_ format, with a column of SNPs as described below.
+The gene dataset is in BED_ format with 12 columns.  The output dataset is also interval.
+(`Dataset missing?`_)
+
+.. _interval: ./static/formatHelp.html#interval
+.. _BED: ./static/formatHelp.html#bed
+.. _Dataset missing?: ./static/formatHelp.html
+
+-----
+
+**What it does**
+
+This tool identifies which SNPs create amino-acid changes in the specified 
+coding regions.  The first input file contains the SNPs and must be an interval file.
+It needs the chromosome, start, and end position as well as the SNP.  The 
+SNP can be given using ambiguous-nucleotide symbols or a list of two to four
+alleles 
+separated by '/'.  Any other columns in the first input file will not be
+used but will be kept for the output.  The second input file contains the genes
+to be used for defining the coding regions.  This file must be a BED file with
+the first 12 columns standard BED columns.  The output is the same as the
+first input file with
+several columns added: the name field from the line of the gene input file
+used, the amino acids, the codon number, and the reference nucleotide that 
+changed in the amino acid.
+The amino acids are listed with the reference amino acid first, then a colon,
+and then the amino acids for the alleles.  If a SNP is not in a coding region
+or is synonymous then it is not included in the output file.
+
+-----
+
+**Example**
+
+- first input file, with SNPs::
+
+    chr22  15660821  15660822  A/G
+    chr22  15825725  15825726  G/T
+    chr22  15827035  15827036  G
+    chr22  15827135  15827136  C/G
+    chr22  15830928  15830929  A/G
+    chr22  15830951  15830952  G
+    chr22  15830955  15830956  C/T
+    chr22  15848885  15848886  C/T
+    chr22  15849048  15849049  A/C
+    chr22  15919711  15919712  A/G
+    etc.
+
+  or, indicating polymorphisms using ambiguous-nucleotide symbols::
+
+    chr22  15660821  15660822  R
+    chr22  15825725  15825726  K
+    chr22  15827035  15827036  G
+    chr22  15827135  15827136  S
+    chr22  15830928  15830929  R
+    chr22  15830951  15830952  G
+    chr22  15830955  15830956  Y
+    chr22  15848885  15848886  Y
+    chr22  15849048  15849049  M
+    chr22  15919711  15919712  R
+    etc.
+
+- second input file, with UCSC annotations for human genes::
+
+    chr22  15688363  15690225  uc010gqr.1  0  +  15688363  15688363  0  2   587,794,  0,1068,
+    chr22  15822826  15869112  uc002zlw.1  0  -  15823622  15869004  0  10  940,105,97,91,265,86,251,208,304,282,  0,1788,2829,3241,4163,6361,8006,26023,29936,46004,
+    chr22  15826991  15869112  uc010gqs.1  0  -  15829218  15869004  0  5   1380,86,157,304,282,  0,2196,21858,25771,41839,
+    chr22  15897459  15919682  uc002zlx.1  0  +  15897459  15897459  0  4   775,128,103,1720,  0,8303,10754,20503,
+    chr22  15945848  15971389  uc002zly.1  0  +  15945981  15970710  0  13  271,25,147,113,127,48,164,84,85,12,102,42,2193,  0,12103,12838,13816,15396,17037,17180,18535,19767,20632,20894,22768,23348,
+    etc.
+
+- output file, showing non-synonymous substitutions in coding regions::
+
+    chr22  15825725  15825726  G/T  uc002zlw.1  Gln:Pro/Gln   469  T
+    chr22  15827035  15827036  G    uc002zlw.1  Glu:Asp       414  C
+    chr22  15827135  15827136  C/G  uc002zlw.1  Gly:Gly/Ala   381  C
+    chr22  15830928  15830929  A/G  uc002zlw.1  Ala:Ser/Pro   281  C
+    chr22  15830951  15830952  G    uc002zlw.1  Leu:Pro       273  A
+    chr22  15830955  15830956  C/T  uc002zlw.1  Ser:Gly/Ser   272  T
+    chr22  15848885  15848886  C/T  uc002zlw.1  Ser:Trp/Stop  217  G
+    chr22  15848885  15848886  C/T  uc010gqs.1  Ser:Trp/Stop  200  G
+    chr22  15849048  15849049  A/C  uc002zlw.1  Gly:Stop/Gly  163  C
+    etc.
+
+  </help>
+</tool>