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1 <tool id="vcfleftalign" name="VCFleftAlign:" version="0.0.1">
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2 <requirements>
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3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
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4 <!-- <requirement type="package" version="0.1.18">samtools</requirement> -->
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5 </requirements>
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6 <description>Left-align indels and complex variants in VCF dataset</description>
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7 <command>
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8 #set $reference_fasta_filename = "localref.fa"
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9 #if str( $reference_source.reference_source_selector ) == "history":
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10 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
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11 #else:
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12 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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13 #end if
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14 vcfleftalign -r "${reference_fasta_filename}" -w "${window_size}" "${input_vcf}" > "${out_file1}"</command>
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15 <inputs>
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16 <param name="input_vcf" type="data" format="vcf" label="VCF dataset to left-align" />
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17 <conditional name="reference_source">
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18 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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19 <option value="cached">Locally cached</option>
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20 <option value="history">History</option>
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21 </param>
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22 <when value="cached">
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23 <param name="ref_file" type="select" label="Select reference genome">
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24 <options from_data_table="fasta_indexes">
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25 </options>
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26 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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27 </param>
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28 </when>
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29 <when value="history"> <!-- FIX ME!!!! -->
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30 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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31 </when>
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32 </conditional>
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33 <param name="window_size" type="integer" value="150" label="Use a window of this many bp when left-aligning" help="default = 150 bp" />
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34 </inputs>
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35 <outputs>
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36 <data format="vcf" name="out_file1" />
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37 </outputs>
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38 <stdio>
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39 <exit_code range="1:" level="fatal" />
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40 </stdio>
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41 <tests>
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42 <test>
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43 <param name="reference_source_selector" value="history" />
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44 <param name="input_vcf" value="vcflib-phix.vcf"/>
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45 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
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46 <param name="window_size" value="150" />
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47 <output name="out_file1" file="vcfleftalign-test1.vcf"/>
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48 </test>
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49 </tests>
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50 <help>
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51
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52 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.
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53
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54 ----
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55
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56 Vcfleftalign is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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57
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58 </help>
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59 </tool>
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