Mercurial > repos > devteam > freebayes
annotate leftalign.xml @ 23:52aed7d9ed2b draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
author | devteam |
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date | Sun, 25 Sep 2016 09:48:24 -0400 |
parents | 978760187fe2 |
children | bf27106652f3 |
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16 | 1 <?xml version="1.0"?> |
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52aed7d9ed2b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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2 <tool id="bamleftalign" name="BamLeftAlign" version="1.0.2.29"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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3 <description> indels in BAM datasets</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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4 <requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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5 <requirement type="package" version="1.0.2.29">freebayes</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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6 <requirement type="package" version="0.1.19">samtools</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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7 </requirements> |
52aed7d9ed2b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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8 <stdio> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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9 <exit_code range="1:" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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10 </stdio> |
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11 <command> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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12 ##set up input files |
52aed7d9ed2b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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13 #set $reference_fasta_filename = "localref.fa" |
52aed7d9ed2b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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14 #if str( $reference_source.reference_source_selector ) == "history": |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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15 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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16 samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for leftalign" >&2 && |
52aed7d9ed2b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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17 #else: |
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18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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19 #end if |
16 | 20 |
23
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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21 ##finished setting up inputs |
52aed7d9ed2b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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22 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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23 ##start leftalign commandline |
52aed7d9ed2b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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24 samtools view -bh "${input_bam}" | bamleftalign |
52aed7d9ed2b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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25 --fasta-reference "${reference_fasta_filename}" |
52aed7d9ed2b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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26 -c |
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27 --max-iterations "${iterations}" |
52aed7d9ed2b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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28 ##outputs |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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29 > "${output_bam}" |
52aed7d9ed2b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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30 </command> |
52aed7d9ed2b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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31 <inputs> |
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32 <conditional name="reference_source"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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33 <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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34 <option value="cached">Locally cached</option> |
52aed7d9ed2b
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35 <option value="history">History</option> |
16 | 36 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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37 <when value="cached"> |
52aed7d9ed2b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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38 <param name="input_bam" type="data" format="bam" label="Select BAM dataset to leftalign"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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39 <validator type="unspecified_build" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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40 <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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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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41 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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42 <param name="ref_file" type="select" label="Using reference genome"> |
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43 <options from_data_table="fasta_indexes"></options> |
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44 <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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45 </param> |
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46 </when> |
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47 <when value="history"> |
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48 <param name="input_bam" type="data" format="bam" label="BAM dataset to re-align" /> |
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49 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> |
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50 </when> |
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51 </conditional> |
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52 <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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53 </inputs> |
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54 <outputs> |
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55 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (alignments)" /> |
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56 </outputs> |
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57 <tests> |
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58 <test> |
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59 <param name="reference_source_selector" value="history" /> |
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60 <param name="ref_file" ftype="fasta" value="leftalign.fa"/> |
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61 <param name="input_bam" ftype="bam" value="left-align-input.bam"/> |
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62 <param name="iterations" value="5"/> |
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63 <output name="output_bam" file="left-align-output.bam" /> |
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64 </test> |
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65 </tests> |
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66 <help> |
16 | 67 |
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. | |
69 | |
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 <citations> |
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73 <citation type="bibtex"> |
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74 @misc{1207.3907, |
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75 Author = {Erik Garrison}, |
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76 Title = {Haplotype-based variant detection from short-read sequencing}, |
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77 Year = {2012}, |
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78 Eprint = {arXiv:1207.3907}, |
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79 url = {http://arxiv.org/abs/1207.3907} |
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80 } |
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81 </citation> |
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82 </citations> |
16 | 83 </tool> |