Mercurial > repos > nilesh > bcftools
comparison bcftools_view.xml @ 2:14567aa2be12 draft default tip
Added wrapper script for correct stderr handling
| author | geert-vandeweyer |
|---|---|
| date | Thu, 10 Apr 2014 09:44:09 -0400 |
| parents | 3182c7fac413 |
| children |
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| 1:3182c7fac413 | 2:14567aa2be12 |
|---|---|
| 1 <tool id="bcftools_view" name="bcftools view" version="1.0.0"> | 1 <tool id="bcftools_view" name="bcftools view" version="1.0.0"> |
| 2 <description>Converts BCF format to VCF format</description> | 2 <description>Converts BCF format to VCF format</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.1.18">samtools</requirement> | 4 <requirement type="package" version="0.1.18">samtools</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command interpreter="python"> | 6 <command interpreter='python'> |
| 7 bcftools view | 7 bcftools_wrapper.py bcftools view |
| 8 #if str( $A ) == "true": | 8 #if str( $A ) == "true": |
| 9 -A | 9 -A |
| 10 #end if | 10 #end if |
| 11 #if str( $b ) == "true": | 11 #if str( $b ) == "true": |
| 12 -b | 12 -b |
| 49 #end if | 49 #end if |
| 50 #if str( $v ) == "true": | 50 #if str( $v ) == "true": |
| 51 -v | 51 -v |
| 52 #end if | 52 #end if |
| 53 $input | 53 $input |
| 54 > $output | 54 > $output |
| 55 </command> | 55 </command> |
| 56 <inputs> | 56 <inputs> |
| 57 <param name="input" type="data" format="bcf" label="Choose a bcf file to view" /> | 57 <param name="input" type="data" format="bcf" label="Choose a bcf file to view" /> |
| 58 <param name="A" type="select" label="Retain all possible alternate alleles at variant sites"> | 58 <param name="A" type="select" label="Retain all possible alternate alleles at variant sites"> |
| 59 <option value="true">Yes</option> | 59 <option value="true">Yes</option> |