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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 12:58:13 +0000
parents 9c4a2ef55965
children
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9c4a2ef55965 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
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1 <tool id="vcfleftalign" name="VCFleftAlign:" version="@WRAPPER_VERSION@+galaxy0">
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f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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2 <description>Left-align indels and complex variants in VCF dataset</description>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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3 <macros>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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4 <import>macros.xml</import>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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5 </macros>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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6 <expand macro="requirements"/>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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7 <expand macro="stdio" />
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50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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8 <command><![CDATA[
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f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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9 #set $reference_fasta_filename = "localref.fa"
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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10 #if str( $reference_source.reference_source_selector ) == "history":
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50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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11 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
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f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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12 #else:
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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13 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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14 #end if
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50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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15 vcfleftalign -r '${reference_fasta_filename}' -w "${window_size}" '${input_vcf}' > '${out_file1}'
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
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16 ]]></command>
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f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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17 <inputs>
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50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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18 <param name="input_vcf" type="data" format="vcf" label="VCF dataset to left-align" />
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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19 <conditional name="reference_source">
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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20 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
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21 <option value="cached">Locally cached</option>
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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22 <option value="history">History</option>
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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23 </param>
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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24 <when value="cached">
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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25 <param name="ref_file" type="select" label="Select reference genome">
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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26 <options from_data_table="fasta_indexes">
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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27 </options>
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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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"/>
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
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29 </param>
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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30 </when>
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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31 <when value="history"> <!-- FIX ME!!!! -->
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
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32 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
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33 </when>
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
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34 </conditional>
50cf7cabae50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
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35 <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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f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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36 </inputs>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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37 <outputs>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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38 <data format="vcf" name="out_file1" />
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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39 </outputs>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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40 <tests>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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41 <test>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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42 <param name="reference_source_selector" value="history" />
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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43 <param name="input_vcf" value="vcflib-phix.vcf"/>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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44 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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45 <param name="window_size" value="150" />
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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46 <output name="out_file1" file="vcfleftalign-test1.vcf"/>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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47 </test>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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48 </tests>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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49 <help>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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51 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.
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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53 ----
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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55 Vcfleftalign @IS_PART_OF_VCFLIB@
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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56 </help>
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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57 <expand macro="citations" />
f0982f54fef1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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58 </tool>