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changes to aaChanges interface

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This commit is contained in:
Richard Burhans
2012-04-02 14:28:08 -04:00
parent be25318d4b
commit c3765659ea
1 changed files with 7 additions and 1 deletions
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tools/evolution/codingSnps.xml
+7 -1
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@@ -2,7 +2,7 @@
<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=$col1 keepColumns=$keep strand=${strand_source.strand_col} > $out_file1
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=$col1 keepColumns=$keep strand=${strand_source.strand_col} unique=$uniqpos > $out_file1
</command>
<inputs>
@@ -17,6 +17,10 @@
<option value="0" selected="true">No</option>
<option value="1">Yes</option>
</param>
<param name="uniqpos" type="select" label="Only report each SNP position once">
<option value="1" selected="true">Yes</option>
<option value="0">No</option>
</param>
<conditional name="strand_source">
<param name="strand_choice" type="select" label="Strand info">
<option value="data_column">a column in the dataset</option>
@@ -54,6 +58,7 @@
<param name="input2" ftype="interval" value="codingSnps_inputGenes1.bed" dbkey="hg18" />
<param name="strand_choice" value="all_pos" />
<param name="strand_col" value="+" />
<param name="uniqpos" value="0" />
<output name="output" file="codingSnps_output1.interval" />
</test>
<test>
@@ -62,6 +67,7 @@
<param name="col1" value="4" />
<param name="strand_choice" value="all_pos" />
<param name="strand_col" value="+" />
<param name="uniqpos" value="0" />
<output name="output" file="codingSnps_output2.interval" />
</test>
<test>