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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 08:10:02 -0500
parents d226a7327946
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d226a7327946 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
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1 <tool id="vcfprimers" name="VCFprimers:" version="@WRAPPER_VERSION@+galaxy0">
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2 <description>Extract flanking sequences for each VCF record</description>
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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3 <macros>
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4 <import>macros.xml</import>
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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5 </macros>
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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6 <expand macro="requirements"/>
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7 <expand macro="stdio" />
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17096387c0e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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8 <command><![CDATA[
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bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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9 #set $reference_fasta_filename = "localref.fa"
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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10 #if str( $reference_source.reference_source_selector ) == "history":
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17096387c0e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers commit 36e9065027cc7bf721e9d203208477ee88906c57"
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11 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
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bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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12 #else:
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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13 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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14 #end if
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17096387c0e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers commit 36e9065027cc7bf721e9d203208477ee88906c57"
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15 vcfprimers -f '${reference_fasta_filename}' -l "${primer_length}" '${input_vcf}' > '${out_file1}'
17096387c0e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers commit 36e9065027cc7bf721e9d203208477ee88906c57"
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16 ]]></command>
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17 <inputs>
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18 <param name="input_vcf" type="data" format="vcf" label="VCF dataset to extract flanks" />
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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19 <conditional name="reference_source">
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20 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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21 <option value="cached">Locally cached</option>
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22 <option value="history">History</option>
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23 </param>
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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24 <when value="cached">
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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25 <param name="ref_file" type="select" label="Select reference genome">
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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26 <options from_data_table="fasta_indexes">
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27 </options>
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17096387c0e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers commit 36e9065027cc7bf721e9d203208477ee88906c57"
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28 <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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bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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29 </param>
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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30 </when>
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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31 <when value="history"> <!-- FIX ME!!!! -->
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32 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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33 </when>
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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34 </conditional>
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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35 <param name="primer_length" type="integer" value="20" label="The length of the primer sequences on each side of the variant" help="default = 20 bp" />
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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36 </inputs>
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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37 <outputs>
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38 <data format="fasta" name="out_file1" />
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="reference_source_selector" value="history" />
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43 <param name="input_vcf" value="vcflib-phix.vcf"/>
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44 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
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45 <param name="primer_length" value="5" />
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46 <output name="out_file1" file="vcfprimers-test1.fasta"/>
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47 </test>
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48 </tests>
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49 <help>
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bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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51 For each VCF record, extract the flanking sequences, and write them as FASTA
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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52 records suitable for alignment. This tool is intended for use in designing validation
bc5949d36b34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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53 experiments. Primers extracted which would flank all of the alleles at multi-allelic
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54 sites. The name of the FASTA "reads" indicates the VCF record which they apply to.
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55 The form is >CHROM_POS_LEFT for the 3' primer and >CHROM_POS_RIGHT for the 5' primer,
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56 for example::
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57
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58 >20_233255_LEFT
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59 CCATTGTATATATAGACCATAATTTCTTTATCCAATCATCTGTTGATGGA
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60 >20_233255_RIGHT
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61 ACTCAGTTGATTCCATACCTTTGCCATCATGAATCATGTTGTAATAAACA
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62
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63 ----
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64
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65 Vcfprimers @IS_PART_OF_VCFLIB@
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66 </help>
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67 <expand macro="citations" />
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68 </tool>