Mercurial > repos > devteam > vcfvcfintersect
annotate vcfvcfintersect.xml @ 2:c7314b925161 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
author | devteam |
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date | Thu, 15 Sep 2016 13:30:27 -0400 |
parents | b29dbe1270b5 |
children | 6f6bf10618d7 |
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2
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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1 <tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="@WRAPPER_VERSION@.0"> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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2 <description>Intersect two VCF datasets</description> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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3 <macros> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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4 <import>macros.xml</import> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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5 </macros> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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6 <expand macro="requirements"/> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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7 <expand macro="stdio" /> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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8 <command> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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9 #set $reference_fasta_filename = "localref.fa" |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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10 #if str( $reference_source.reference_source_selector ) == "history": |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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11 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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12 #else: |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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13 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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14 #end if |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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15 |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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16 #if $adv_options.adv_options_selector == "use_adv_controls": |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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17 vcfintersect "${adv_options.adv_options_input}" ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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18 #else: |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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19 vcfintersect ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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20 #end if |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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21 </command> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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22 <inputs> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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23 <!-- selecting refernce source --> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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24 <param name="vcf_input1" type="data" format="vcf" label="The first VCF dataset" /> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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25 <param name="vcf_input2" type="data" format="vcf" label="The second VCF dataset" |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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26 help="The second dataset will be instersected with the first"/> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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27 <conditional name="reference_source"> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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28 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome" |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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29 help="This tools needs to access reference genomes sequence specified by this option."> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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30 <option value="cached">Locally cached</option> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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31 <option value="history">History</option> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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32 </param> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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33 <when value="cached"> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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34 <param name="ref_file" type="select" label="Select reference genome"> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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35 <options from_data_table="fasta_indexes"> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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36 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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37 </options> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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38 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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39 </param> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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40 </when> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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41 <when value="history"> <!-- FIX ME!!!! --> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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42 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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43 </when> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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44 </conditional> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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45 <param name="isect_union" type="select" label="Union or intersection" help="-i or -u"> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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46 <option value="-i">Intersect</option> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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47 <option value="-u">Union</option> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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48 </param> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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49 <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert" /> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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50 <param name="window_size" type="integer" value="30" |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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51 label="compare records up to this many bp away (window size)" help="-w, --window-size" /> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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52 <param name="loci" type="boolean" truevalue="-l" falsevalue="" |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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53 label="output whole loci when one alternate allele matches" help="-l, --loci" /> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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54 <conditional name="adv_options"> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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55 <param name="adv_options_selector" type="select" label="Advanced controls" help="Allows you to specify options that are not listed above"> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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56 <option value="no">Don't use advanced options</option> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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57 <option value="use_adv_controls">Use advanced options</option> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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58 </param> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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59 <when value="no" /> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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60 <when value="use_adv_controls"> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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61 <param name="adv_options_input" type="text" value="-t "vcfvcf-intersect-result"" |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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62 label="Enter additional command line options described in the help section below" |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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63 help="such as -m, -t, -V, -M, and -T" /> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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64 <sanitizer> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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65 <valid initial="string.printable"> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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66 <remove value="'"/> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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67 </valid> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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68 <mapping initial="none"> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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69 <add source="'" target="__sq__"/> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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70 </mapping> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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71 </sanitizer> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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72 </when> |
c7314b925161
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
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73 </conditional> |
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74 </inputs> |
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75 <outputs> |
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76 <data format="vcf" name="out_file1" /> |
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77 </outputs> |
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78 <tests> |
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79 <test> |
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80 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> |
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81 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> |
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82 <param name="reference_source_selector" value="history" /> |
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83 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> |
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84 <param name="isect_union" value="-i" /> |
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85 <param name="invert" value="False" /> |
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86 <param name="loci" value="False" /> |
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87 <patam name="adv_options_selector" value="no" /> |
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88 <param name="window_size" value="30" /> |
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89 <output name="out_file1" file="vcfvcfintersect-test1.vcf"/> |
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90 </test> |
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91 <test> |
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92 <param name="reference_source_selector" value="history" /> |
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93 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> |
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94 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> |
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95 <param name="isect_union" value="-u" /> |
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96 <param name="invert" value="False" /> |
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97 <param name="loci" value="False" /> |
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98 <patam name="adv_options_selector" value="no" /> |
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99 <param name="window_size" value="30" /> |
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100 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> |
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101 <output name="out_file1" file="vcfvcfintersect-test2.vcf"/> |
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102 </test> |
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103 </tests> |
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104 <help> |
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105 Computes intersections and unions for two VCF datasets. Unifies equivalent alleles within window-size bp. |
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106 |
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107 The options are:: |
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108 |
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109 -v, --invert invert the selection, printing only records which would |
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110 -i, --intersect-vcf FILE use this VCF for set intersection generation |
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111 -u, --union-vcf FILE use this VCF for set union generation |
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112 -w, --window-size N compare records up to this many bp away (default 30) |
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113 -l, --loci output whole loci when one alternate allele matches |
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114 -m, --ref-match intersect on the basis of record REF string |
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115 -t, --tag TAG attach TAG to each record's info field if it would intersect |
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116 -V, --tag-value VAL use this value to indicate that the allele is passing |
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117 '.' will be used otherwise. default: 'PASS' |
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118 -M, --merge-from FROM-TAG |
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119 -T, --merge-to TO-TAG merge from FROM-TAG used in the -i file, setting TO-TAG |
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120 in the current file. |
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121 |
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122 ---- |
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123 |
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124 VCFVCFintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). |
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125 </help> |
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126 <expand macro="citations" /> |
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127 </tool> |