Mercurial > repos > iuc > vt_variant_tools
changeset 3:4ffcf0672e81 draft
Uploaded
| author | bgruening |
|---|---|
| date | Thu, 14 Aug 2014 07:40:02 -0400 |
| parents | b1a42223e9f9 |
| children | bb468ee178d8 |
| files | vt_normalize.xml |
| diffstat | 1 files changed, 30 insertions(+), 8 deletions(-) [+] |
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--- a/vt_normalize.xml Thu Aug 14 06:18:37 2014 -0400 +++ b/vt_normalize.xml Thu Aug 14 07:40:02 2014 -0400 @@ -12,9 +12,19 @@ -o "${ outfile }" ##-q do not print options and summary [] -w window size for local sorting of variants [10000] - -I $intervals_file + + #if str( $intervals_file ) != 'None': + -I "${intervals_file}" + #end if + ##-i intervals [] - -r $reference_genome + + #if $reference_source.reference_source_selector != "history": + -r "${reference_source.reference_genome.fields.path}"' + #else: + -r "${reference_source.reference_genome}" + #end if + "${ infile }" ]]> </command> @@ -22,12 +32,24 @@ <inputs> <param name="infile" type="data" format="vcf" label="VCF file to be normalised" /> - <param name="reference_genome" type="select" label="Using reference genome"> - <options from_data_table="fasta_indexes"> - <filter type="data_meta" ref="infile" key="dbkey" column="1" /> - <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> - </options> - </param> + + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> + <option value="cached" selected="True">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="reference_genome" type="select" label="Using reference genome"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="infile" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options> + </param> + </when> + <when value="history"> + <param name="reference_genome" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> <param name="intervals_file" type="data" format="bed" optional="True" label="File containing list of intervals" /> <param name="window" type="integer" value="10000" size="10" label="Window size for local sorting of variants"