Mercurial > repos > greg > affy2vcf

comparison affy2vcf.xml @ 15:5b64c88d706f draft default tip

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author greg
date Fri, 30 Nov 2018 08:22:38 -0500
parents 640d50a57063
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14:640d50a57063 15:5b64c88d706f
12 mkdir $text_outputs_dir && 12 mkdir $text_outputs_dir &&
13 bcftools +\$BCFTOOLS_PLUGINS/affy2vcf.so 13 bcftools +\$BCFTOOLS_PLUGINS/affy2vcf.so
14 #if str($reference_genome_source_cond.reference_genome_source) == "history": 14 #if str($reference_genome_source_cond.reference_genome_source) == "history":
15 --fasta-ref '$reference_genome_source_cond.history_item' 15 --fasta-ref '$reference_genome_source_cond.history_item'
16 #else: 16 #else:
17 --fasta-ref '$reference_genome_source_cond.locally_cached_item' 17 --fasta-ref '$reference_genome_source_cond.locally_cached_item.fields.path'
18 #end if 18 #end if
19 --annot '$annot' 19 --annot '$annot'
20 --snp-posteriors '$snp_posteriors' 20 --snp-posteriors '$snp_posteriors'
21 --summary '$summary' 21 --summary '$summary'
22 --report '$report' 22 --report '$report'
48 <param name="history_item" type="data" format="fasta" label="Select reference genome" /> 48 <param name="history_item" type="data" format="fasta" label="Select reference genome" />
49 </when> 49 </when>
50 <when value="cached"> 50 <when value="cached">
51 <param name="locally_cached_item" type="select" format="fasta" label="Fasta reference sequence"> 51 <param name="locally_cached_item" type="select" format="fasta" label="Fasta reference sequence">
52 <options from_data_table="all_fasta"> 52 <options from_data_table="all_fasta">
53 <column name="name" index="1"/> 53 <column name="name" index="2"/>
54 <column name="value" index="2"/> 54 <column name="value" index="0"/>
55 <column name="path" index="2"/> 55 <column name="path" index="3"/>
56 <filter type="sort_by" column="1"/> 56 <filter type="sort_by" column="1"/>
57 <validator type="no_options" message="No cached Fasta genome references are available for the build associated with the selected probeset annotation file." /> 57 <validator type="no_options" message="No cached Fasta genome references are available for the build associated with the selected probeset annotation file." />
58 </options> 58 </options>
59 </param> 59 </param>
60 </when> 60 </when>