Mercurial > repos > devteam > picard
annotate picard_MergeBamAlignment.xml @ 26:fc3866ddc7b6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 0244aa33464cc27d1ce881cb310b8eda36e9a89c
author | iuc |
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date | Mon, 22 Aug 2022 09:54:37 +0000 |
parents | a5a13ea16d17 |
children | fdca9493e09b |
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486d7500da69
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
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1 <tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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2 <description>merge alignment data with additional info stored in an unmapped BAM dataset</description> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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3 <macros> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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4 <import>picard_macros.xml</import> |
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a5a13ea16d17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
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5 <token name="@WRAPPER_VERSION@">1</token> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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6 </macros> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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7 <expand macro="requirements" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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8 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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9 @java_options@ |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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10 #set $picard_dict = "localref.dict" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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11 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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12 |
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08f69add4d06
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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13 ln -s "${reference_source.ref_file}" "${ref_fasta}" && |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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14 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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15 #if str( $reference_source.reference_source_selector ) == "history": |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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16 |
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08f69add4d06
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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17 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" |
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52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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18 QUIET=true |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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19 VERBOSITY=ERROR |
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a5a13ea16d17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
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20 @TMPDIR_OPTION@ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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21 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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22 && |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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23 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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24 #else: |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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25 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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26 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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27 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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28 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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29 |
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08f69add4d06
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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30 picard |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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31 MergeBamAlignment |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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32 UNMAPPED_BAM="${unmapped_bam}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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33 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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34 PAIRED_RUN=true ##This argument is ignored and will be removed. Required. Possible values: {true, false} |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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35 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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36 #if str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_one_file": |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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37 #for $dataset in $aligned_or_read1_and_read2.aligned_bams: |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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38 ALIGNED_BAM="${dataset.aligned_bam}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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39 #end for |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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40 #elif str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_two_files": |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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41 #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams: |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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42 READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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43 #end for |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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44 #for $dataset in $aligned_or_read1_and_read2.read2_aligned_bams: |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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45 READ2_ALIGNED_BAM="${dataset.read2_aligned_bam}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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46 #end for |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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47 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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48 #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams: |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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49 READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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50 #end for |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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51 #end if |
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52 |
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53 OUTPUT="${outFile}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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54 REFERENCE_SEQUENCE="${ref_fasta}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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55 |
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56 CLIP_ADAPTERS="${clip_adapters}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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57 IS_BISULFITE_SEQUENCE="${is_bisulfite_sequence}" |
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58 ALIGNED_READS_ONLY="${aligned_reads_only}" |
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59 MAX_INSERTIONS_OR_DELETIONS="${max_insertions_or_deletions}" |
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60 |
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61 #for $attribute in $attributes_to_retain: |
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62 ATTRIBUTES_TO_RETAIN="${$attribute.attribute}" |
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63 #end for |
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64 |
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65 #for $attribute in $attributes_to_remove: |
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66 ATTRIBUTES_TO_REMOVE="${$attribute.attribute}" |
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67 #end for |
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68 |
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69 READ1_TRIM="${read1_trim}" |
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70 READ2_TRIM="${read2_trim}" |
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71 |
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72 #if str( $orientations ) != "None": |
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73 #for $orientation in str( $orientations ).split(','): ## See trello card https://trello.com/c/9nW02Zhd |
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74 EXPECTED_ORIENTATIONS="${orientation}" |
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75 #end for |
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76 #end if |
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77 |
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78 ALIGNER_PROPER_PAIR_FLAGS="${aligner_proper_pair_flags}" |
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79 PRIMARY_ALIGNMENT_STRATEGY="${primary_alignment_strategy}" |
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80 CLIP_OVERLAPPING_READS="${clip_overlapping_reads}" |
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81 INCLUDE_SECONDARY_ALIGNMENTS="${include_secondary_alignments}" |
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82 ADD_MATE_CIGAR="${add_mate_cigar}" |
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83 |
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84 VALIDATION_STRINGENCY="${validation_stringency}" |
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85 |
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86 SORT_ORDER=coordinate |
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87 QUIET=true |
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88 VERBOSITY=ERROR |
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89 @TMPDIR_OPTION@ |
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90 |
7
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91 ]]></command> |
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92 |
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93 <inputs> |
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94 |
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95 <conditional name="reference_source"> |
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96 <param name="reference_source_selector" type="select" label="Load reference genome from"> |
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97 <option value="cached">Local cache</option> |
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98 <option value="history">History</option> |
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99 </param> |
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100 <when value="cached"> |
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101 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> |
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102 <options from_data_table="picard_indexes"> |
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103 <filter type="sort_by" column="2" /> |
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104 <validator type="no_options" message="No indexes are available" /> |
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105 </options> |
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106 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> |
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107 </param> |
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108 </when> |
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109 <when value="history"> |
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110 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" /> |
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111 </when> |
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112 </conditional> |
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113 |
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114 <param format="sam,bam" name="unmapped_bam" type="data" label="Selected unaligned SAM or BAM with original reads" help="UNMAPPED_BAM; This dataset must be sorted in queryname order (use picard_SortSam to do this)" /> |
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115 <conditional name="aligned_or_read1_and_read2"> |
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116 <param name="aligned_or_read1_and_read2_selector" type="select" label="What type of aligned data do you have?"> |
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117 <option value="paired_one_file">Paired data in a single BAM file (ALIGNED_BAM)</option> |
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118 <option value="paired_two_files">Paired data in separate files (READ1_ALIGNED_BAM and READ2_ALIGNED_BAM)</option> |
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119 <option value="single_file">Singe end data (READ1_ALIGNED_BAM)</option> |
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120 </param> |
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121 <when value="paired_one_file"> |
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122 <repeat name="aligned_bams" title="Aligned SAM or BAM dataset" min="1" help="You can provide multiple datasets"> |
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123 <param name="aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data" help="ALIGNED_BAM"/> |
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124 </repeat> |
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125 </when> |
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126 <when value="paired_two_files"> |
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127 <repeat name="read1_aligned_bams" title="Aligned SAM or BAM dataset for Read 1" min="1" help="You can provide multiple datasets"> |
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128 <param name="read1_aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data for Read1" help="READ1_ALIGNED_BAM"/> |
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129 </repeat> |
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130 <repeat name="read2_aligned_bams" title="Aligned SAM or BAM dataset for Read 2" min="1" help="You can provide multiple datasets"> |
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131 <param name="read2_aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data for Read2" help="READ2_ALIGNED_BAM"/> |
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132 </repeat> |
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133 </when> |
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134 <when value="single_file"> |
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135 <repeat name="read1_aligned_bams" title="Aligned SAM or BAM dataset for Single Reads" min="1" help="You can provide multiple datasets"> |
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136 <param name="read1_aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data" help="READ1_ALIGNED_BAM"/> |
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137 </repeat> |
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138 </when> |
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139 </conditional> |
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140 |
3
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141 <param name="clip_adapters" type="boolean" checked="true" label="Whether to clip adapters where identified" help="CLIP_ADAPTERS; default=True"/> |
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142 <param name="is_bisulfite_sequence" type="boolean" label="Whether the data is from bisulfite sequencing (used when caculating the NM tag)" help="IS_BISULFITE_SEQUENCE; default=False"/> |
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143 <param name="aligned_reads_only" type="boolean" label="Whether to output only aligned reads" help="ALIGNED_READS_ONLY; default=False"/> |
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144 <param name="max_insertions_or_deletions" type="integer" value="1" label="The maximum number of insertions or deletions permitted for an alignment to be included" help="MAX_INSERTIONS_OR_DELETIONS; Alignments with more than this many insertions or deletions will be ignored. Set to -1 to allow any number of insertions or deletions. default=1"/> |
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145 |
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146 <repeat name="attributes_to_retain" title="Retain the following alignment attribute" min="0" help="You can provide multiple attributes"> |
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147 <param name="attribute" type="text" label="Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over from the alignment data when merging" help="ATTRIBUTES_TO_RETAIN; example: XA"/> |
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148 </repeat> |
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149 |
3
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150 <repeat name="attributes_to_remove" title="Remove the following alignment attribute" min="0" help="You can provide multiple attributes"> |
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151 <param name="attribute" type="text" label="Attributes from the alignment record that should be removed when merging." help="ATTRIBUTES_TO_REMOVE; This overrides ATTRIBUTES_TO_RETAIN if they share common tags"/> |
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152 </repeat> |
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153 |
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154 <param name="read1_trim" type="integer" value="0" label="The number of bases trimmed from the beginning of read 1 prior to alignment" help="READ1_TRIM; default=0"/> |
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155 <param name="read2_trim" type="integer" value="0" label="The number of bases trimmed from the beginning of read 2 prior to alignment" help="READ2_TRIM; default=0"/> |
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156 |
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157 <param name="orientations" type="select" multiple="True" display="checkboxes" label="The expected orientation of proper read pairs" help="EXPECTED_ORIENTATIONS; multiple orinetations can be selected"> |
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158 <option value="FR">Forward/Reverse (FR)</option> |
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159 <option value="RF">Reverse/Forward (RF)</option> |
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160 <option value="TANDEM">Tandem</option> |
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161 </param> |
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162 |
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163 |
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164 <param name="aligner_proper_pair_flags" type="boolean" label="Use the aligner's idea of what a proper pair is rather than computing in this program" help="ALIGNER_PROPER_PAIR_FLAGS; default=False"/> |
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165 |
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166 <param name="primary_alignment_strategy" type="select" label="Strategy for selecting primary alignment when the aligner has provided more than one alignment for a pair or fragments" help="PRIMARY_ALIGNMENT_STRATEGY; see help below for more info; default=BestMapq"> |
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167 <option value="BestMapq" selected="True">BestMapq</option> |
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168 <option value="EarliestFragment">EarliestFragment</option> |
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169 <option value="BestEndMapq">BestEndMapq</option> |
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170 <option value="MostDistant">MostDistant</option> |
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171 </param> |
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172 |
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173 <param name="clip_overlapping_reads" type="boolean" checked="True" label="For paired reads, soft clip the 3' end of each read if necessary so that it does not extend past the 5' end of its mate" help="CLIP_OVERLAPPING_READS; default=True"/> |
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174 <param name="include_secondary_alignments" type="boolean" checked="True" label="If false, do not write secondary alignments to output" help="INCLUDE_SECONDARY_ALIGNMENTS; default=True"/> |
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175 <param name="add_mate_cigar" type="boolean" checked="True" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/> |
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176 <expand macro="VS" /> |
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177 </inputs> |
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178 <outputs> |
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179 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with merged alignments"/> |
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180 </outputs> |
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181 <tests> |
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182 <test> |
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183 <param name="reference_source_selector" value="history" /> |
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184 <param name="ref_file" value="picard_MergeBamAlignment_ref.fa" ftype="fasta" /> |
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185 <param name="unmapped_bam" value="picard_MergeBamAlignment_unaligned.bam" ftype="bam"/> |
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186 <param name="aligned_or_read1_and_read2_selector" value="paired_one_file"/> |
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187 <param name="aligned_bam" value="picard_MergeBamAlignment_aligned.bam" ftype="bam"/> |
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188 <param name="clip_adapters" value="True"/> |
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189 <param name="is_bisulfite_sequence" value="False"/> |
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190 <param name="aligned_reads_only" value="False"/> |
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191 <param name="max_insertions_or_deletions" value="1"/> |
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192 <param name="read1_trim" value="0"/> |
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193 <param name="read2_trim" value="0"/> |
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194 <param name="orientation" value="FR"/> |
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195 <param name="aligner_proper_pair_flags" value="False"/> |
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196 <param name="primary_alignment_strategy" value="BestMapq"/> |
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197 <param name="clip_overlapping_reads" value="True"/> |
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198 <param name="include_secondary_alignments" value="True"/> |
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199 <param name="add_mate_cigar" value="True"/> |
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200 <output name="outFile" file="picard_MergeBamAlignment_test1.bam" ftype="bam" lines_diff="4"/> |
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201 </test> |
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202 </tests> |
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203 |
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204 |
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205 <help> |
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206 |
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207 .. class:: infomark |
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208 |
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209 **Purpose** |
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210 |
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211 Merges alignment data from a SAM or BAM dataset with additional data stored in an unmapped BAM dataset and produces a third SAM or BAM dataset of aligned and unaligned reads. |
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212 |
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213 @dataset_collections@ |
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214 |
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215 @description@ |
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216 |
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217 UNMAPPED_BAM=File |
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218 UNMAPPED=File Original SAM or BAM file of unmapped reads, which must be in queryname order. Required. |
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219 |
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220 ALIGNED_BAM=File |
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221 ALIGNED=File SAM or BAM file(s) with alignment data. This option may be specified 0 or more times. |
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222 Cannot be used in conjuction with option(s) READ1_ALIGNED_BAM (R1_ALIGNED) |
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223 READ2_ALIGNED_BAM (R2_ALIGNED) |
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224 |
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225 READ1_ALIGNED_BAM=File |
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226 R1_ALIGNED=File SAM or BAM file(s) with alignment data from the first read of a pair. This option may be |
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227 specified 0 or more times. Cannot be used in conjuction with option(s) ALIGNED_BAM |
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228 (ALIGNED) |
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229 |
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230 READ2_ALIGNED_BAM=File |
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231 R2_ALIGNED=File SAM or BAM file(s) with alignment data from the second read of a pair. This option may |
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232 be specified 0 or more times. Cannot be used in conjuction with option(s) ALIGNED_BAM |
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233 (ALIGNED) |
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234 |
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235 PAIRED_RUN=Boolean |
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236 PE=Boolean This argument is ignored and will be removed. Required. Possible values: {true, false} |
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237 |
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238 JUMP_SIZE=Integer |
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239 JUMP=Integer The expected jump size (required if this is a jumping library). Deprecated. Use |
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240 EXPECTED_ORIENTATIONS instead Default value: null. Cannot be used in conjuction with |
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241 option(s) EXPECTED_ORIENTATIONS (ORIENTATIONS) |
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242 |
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243 CLIP_ADAPTERS=Boolean Whether to clip adapters where identified. Default value: true. Possible values: {true, false} |
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244 |
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245 IS_BISULFITE_SEQUENCE=Boolean Whether the lane is bisulfite sequence (used when caculating the NM tag). Default value: |
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246 false. Possible values: {true, false} |
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247 |
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248 ALIGNED_READS_ONLY=Boolean Whether to output only aligned reads. Default value: false. Possible values: {true, false} |
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249 |
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250 MAX_INSERTIONS_OR_DELETIONS=Integer |
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251 MAX_GAPS=Integer The maximum number of insertions or deletions permitted for an alignment to be included. |
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252 Alignments with more than this many insertions or deletions will be ignored. Set to -1 to |
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253 allow any number of insertions or deletions. Default value: 1. |
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254 |
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255 ATTRIBUTES_TO_RETAIN=String Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over |
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256 from the alignment data when merging. This option may be specified 0 or more times. |
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257 |
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258 ATTRIBUTES_TO_REMOVE=String Attributes from the alignment record that should be removed when merging. This overrides |
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259 ATTRIBUTES_TO_RETAIN if they share common tags. This option may be specified 0 or more |
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260 times. |
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261 |
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262 READ1_TRIM=Integer |
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263 R1_TRIM=Integer The number of bases trimmed from the beginning of read 1 prior to alignment Default |
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264 value: 0. |
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265 |
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266 READ2_TRIM=Integer |
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267 R2_TRIM=Integer The number of bases trimmed from the beginning of read 2 prior to alignment Default |
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268 value: 0. |
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269 |
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270 EXPECTED_ORIENTATIONS=PairOrientation |
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271 ORIENTATIONS=PairOrientation The expected orientation of proper read pairs. Replaces JUMP_SIZE Possible values: {FR, |
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272 RF, TANDEM} This option may be specified 0 or more times. Cannot be used in conjuction |
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273 with option(s) JUMP_SIZE (JUMP) |
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274 |
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275 ALIGNER_PROPER_PAIR_FLAGS=Boolean |
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276 Use the aligner's idea of what a proper pair is rather than computing in this program. |
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277 Default value: false. Possible values: {true, false} |
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278 |
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279 SORT_ORDER=SortOrder |
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280 SO=SortOrder The order in which the merged reads should be output. Default value: coordinate. |
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281 Possible values: {unsorted, queryname, coordinate} |
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282 |
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283 PRIMARY_ALIGNMENT_STRATEGY=PrimaryAlignmentStrategy |
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284 Strategy for selecting primary alignment when the aligner has provided more than one |
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285 alignment for a pair or fragment, and none are marked as primary, more than one is marked |
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286 as primary, or the primary alignment is filtered out for some reason. BestMapq expects |
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287 that multiple alignments will be correlated with HI tag, and prefers the pair of |
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288 alignments with the largest MAPQ, in the absence of a primary selected by the aligner. |
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289 EarliestFragment prefers the alignment which maps the earliest base in the read. Note |
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290 that EarliestFragment may not be used for paired reads. BestEndMapq is appropriate for |
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291 cases in which the aligner is not pair-aware, and does not output the HI tag. It simply |
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292 picks the alignment for each end with the highest MAPQ, and makes those alignments |
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293 primary, regardless of whether the two alignments make sense together.MostDistant is also |
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294 for a non-pair-aware aligner, and picks the alignment pair with the largest insert size. |
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295 If all alignments would be chimeric, it picks the alignments for each end with the best |
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296 MAPQ. For all algorithms, ties are resolved arbitrarily. Default value: BestMapq. |
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297 Possible values: {BestMapq, EarliestFragment, BestEndMapq, MostDistant} |
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298 |
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299 CLIP_OVERLAPPING_READS=BooleanFor paired reads, soft clip the 3' end of each read if necessary so that it does not |
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300 extend past the 5' end of its mate. Default value: true. Possible values: {true, false} |
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301 |
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302 INCLUDE_SECONDARY_ALIGNMENTS=Boolean |
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303 If false, do not write secondary alignments to output. Default value: true. |
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304 Possible values: {true, false} |
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305 |
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306 ADD_MATE_CIGAR=Boolean |
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307 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Possible values: {true, false} |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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308 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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309 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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310 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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311 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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312 @more_info@ |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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313 </help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
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314 <expand macro="citations" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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315 </tool> |