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annotate leftalign.xml @ 3:9f3d6c3098ac draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:37:39 -0500
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9f3d6c3098ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <?xml version="1.0"?>
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2 <tool id="bamleftalign" name="BamLeftAlign" version="0.4">
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3 <requirements>
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4 <requirement type="package" version="0_9_20_b040236">freebayes</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 </requirements>
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7 <description> indels in BAM datasets</description>
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8 <command>
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9 ##set up input files
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10 #set $reference_fasta_filename = "localref.fa"
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11 #if str( $reference_source.reference_source_selector ) == "history":
9f3d6c3098ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
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13 samtools faidx "${reference_fasta_filename}" 2&gt;&amp;1 || echo "Error running samtools faidx for leftalign" &gt;&amp;2 &amp;&amp;
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14 #else:
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15 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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16 #end if
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17
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18 ##finished setting up inputs
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19
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20 ##start leftalign commandline
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21 samtools view -bh "${input_bam}" | bamleftalign
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22 --fasta-reference "${reference_fasta_filename}"
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23 -c
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24 --max-iterations "${iterations}"
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25 ##outputs
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26 > "${output_bam}"
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27 </command>
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28 <inputs>
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29 <conditional name="reference_source">
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30 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
9f3d6c3098ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 <option value="cached">Locally cached</option>
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32 <option value="history">History</option>
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33 </param>
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34 <when value="cached">
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35 <param name="input_bam" type="data" format="bam" label="Select BAM dataset to leftalign">
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36 <validator type="unspecified_build" />
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37 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
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38 </param>
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39 <param name="ref_file" type="select" label="Using reference genome">
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40 <options from_data_table="fasta_indexes"></options>
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41 <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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42 </param>
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43 </when>
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44 <when value="history">
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45 <param name="input_bam" type="data" format="bam" label="BAM dataset to re-align" />
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46 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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47 </when>
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48 </conditional>
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49 <param name="iterations" type="integer" value="5" label="Maximum number of iterations" help="Iterate the left-realignment no more than this many times" />
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50 </inputs>
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51 <outputs>
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52 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (alignments)" />
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="reference_source_selector" value="history" />
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57 <param name="ref_file" ftype="fasta" value="leftalign.fa"/>
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58 <param name="input_bam" ftype="bam" value="left-align-input.bam"/>
9f3d6c3098ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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59 <param name="iterations" value="5"/>
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60 <output name="output_bam" file="left-align-output.bam" />
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61 </test>
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62 </tests>
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63 <stdio>
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64 <exit_code range="1:" />
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65 </stdio>
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66 <help>
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67
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68 When calling indels, it is important to homogenize the positional distribution of insertions and deletions in the input by using left realignment. Left realignment will place all indels in homopolymer and microsatellite repeats at the same position, provided that doing so does not introduce mismatches between the read and reference other than the indel. This method is computationally inexpensive and handles the most common classes of alignment inconsistency.
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69
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70 This is leftalign utility from FreeBayes package developed and maintained by Erik Garrison (https://github.com/ekg/freebayes).
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71 </help>
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72
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73 <citations>
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74 <citation type="bibtex">
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75 @misc{1207.3907,
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76 Author = {Erik Garrison},
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77 Title = {Haplotype-based variant detection from short-read sequencing},
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78 Year = {2012},
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79 Eprint = {arXiv:1207.3907},
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80 url = {http://arxiv.org/abs/1207.3907}
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81 }
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82 </citation>
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83 </citations>
9f3d6c3098ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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84
9f3d6c3098ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
85 </tool>