Mercurial > repos > devteam > vcfleftalign
comparison vcfleftalign.xml @ 0:3e3d0dffeb1f draft
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| author | devteam |
|---|---|
| date | Thu, 19 Mar 2015 14:41:53 -0400 |
| parents | |
| children | 8e02d116b0f9 |
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| -1:000000000000 | 0:3e3d0dffeb1f |
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| 1 <tool id="vcfleftalign" name="VCFleftAlign:" version="0.0.3"> | |
| 2 <description>Left-align indels and complex variants in VCF dataset</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"></expand> | |
| 7 <expand macro="stdio"></expand> | |
| 8 <command> | |
| 9 #set $reference_fasta_filename = "localref.fa" | |
| 10 #if str( $reference_source.reference_source_selector ) == "history": | |
| 11 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && | |
| 12 #else: | |
| 13 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | |
| 14 #end if | |
| 15 vcfleftalign -r "${reference_fasta_filename}" -w "${window_size}" "${input_vcf}" > "${out_file1}"</command> | |
| 16 <inputs> | |
| 17 <param name="input_vcf" type="data" format="vcf" label="VCF dataset to left-align" /> | |
| 18 <conditional name="reference_source"> | |
| 19 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
| 20 <option value="cached">Locally cached</option> | |
| 21 <option value="history">History</option> | |
| 22 </param> | |
| 23 <when value="cached"> | |
| 24 <param name="ref_file" type="select" label="Select reference genome"> | |
| 25 <options from_data_table="fasta_indexes"> | |
| 26 </options> | |
| 27 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 28 </param> | |
| 29 </when> | |
| 30 <when value="history"> <!-- FIX ME!!!! --> | |
| 31 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
| 32 </when> | |
| 33 </conditional> | |
| 34 <param name="window_size" type="integer" value="150" label="Use a window of this many bp when left-aligning" help="default = 150 bp" /> | |
| 35 </inputs> | |
| 36 <outputs> | |
| 37 <data format="vcf" name="out_file1" /> | |
| 38 </outputs> | |
| 39 <tests> | |
| 40 <test> | |
| 41 <param name="reference_source_selector" value="history" /> | |
| 42 <param name="input_vcf" value="vcflib-phix.vcf"/> | |
| 43 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> | |
| 44 <param name="window_size" value="150" /> | |
| 45 <output name="out_file1" file="vcfleftalign-test1.vcf"/> | |
| 46 </test> | |
| 47 </tests> | |
| 48 <help> | |
| 49 | |
| 50 Left-aligns variants in VCF dataset. Window size is determined dynamically according to the entropy of the regions flanking the indel. These must have entropy > 1 bit/bp, or be shorter than ~5kb. | |
| 51 | |
| 52 ---- | |
| 53 | |
| 54 Vcfleftalign @IS_PART_OF_VCFLIB@ | |
| 55 </help> | |
| 56 <expand macro="citations" /> | |
| 57 </tool> |