Mercurial > repos > iuc > vt_variant_tools

comparison vt_normalize.xml @ 3:4ffcf0672e81 draft

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Uploaded
author bgruening
date Thu, 14 Aug 2014 07:40:02 -0400
parents a5578ce1c0a1
children bb468ee178d8
comparison
equal deleted inserted replaced
2:b1a42223e9f9 3:4ffcf0672e81
10 <![CDATA[ 10 <![CDATA[
11 vt @BINARY@ 11 vt @BINARY@
12 -o "${ outfile }" 12 -o "${ outfile }"
13 ##-q do not print options and summary [] 13 ##-q do not print options and summary []
14 -w window size for local sorting of variants [10000] 14 -w window size for local sorting of variants [10000]
15 -I $intervals_file 15
16 #if str( $intervals_file ) != 'None':
17 -I "${intervals_file}"
18 #end if
19
16 ##-i intervals [] 20 ##-i intervals []
17 -r $reference_genome 21
22 #if $reference_source.reference_source_selector != "history":
23 -r "${reference_source.reference_genome.fields.path}"'
24 #else:
25 -r "${reference_source.reference_genome}"
26 #end if
27
18 "${ infile }" 28 "${ infile }"
19 ]]> 29 ]]>
20 </command> 30 </command>
21 <expand macro="stdio" /> 31 <expand macro="stdio" />
22 <inputs> 32 <inputs>
23 <param name="infile" type="data" format="vcf" label="VCF file to be normalised" /> 33 <param name="infile" type="data" format="vcf" label="VCF file to be normalised" />
24 34
25 <param name="reference_genome" type="select" label="Using reference genome"> 35
26 <options from_data_table="fasta_indexes"> 36 <conditional name="reference_source">
27 <filter type="data_meta" ref="infile" key="dbkey" column="1" /> 37 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
28 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> 38 <option value="cached" selected="True">Locally cached</option>
29 </options> 39 <option value="history">History</option>
30 </param> 40 </param>
41 <when value="cached">
42 <param name="reference_genome" type="select" label="Using reference genome">
43 <options from_data_table="fasta_indexes">
44 <filter type="data_meta" ref="infile" key="dbkey" column="1" />
45 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
46 </options>
47 </param>
48 </when>
49 <when value="history">
50 <param name="reference_genome" type="data" format="fasta" label="Using reference file" />
51 </when>
52 </conditional>
31 53
32 <param name="intervals_file" type="data" format="bed" optional="True" label="File containing list of intervals" /> 54 <param name="intervals_file" type="data" format="bed" optional="True" label="File containing list of intervals" />
33 <param name="window" type="integer" value="10000" size="10" label="Window size for local sorting of variants" 55 <param name="window" type="integer" value="10000" size="10" label="Window size for local sorting of variants"
34 help="(-w)"> 56 help="(-w)">
35 <validator type="in_range" min="0"/> 57 <validator type="in_range" min="0"/>