Mercurial > repos > devteam > samtools_calmd
annotate samtools_calmd.xml @ 2:e65c2cd0964c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
author | iuc |
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date | Fri, 30 Nov 2018 17:46:15 -0500 |
parents | 33208952b99d |
children | 3d873744df7e |
rev | line source |
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e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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1 <tool id="samtools_calmd" name="CalMD" version="2.0.2"> |
1
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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2 <description>recalculate MD/NM tags</description> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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3 <macros> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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4 <import>macros.xml</import> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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5 </macros> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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6 <expand macro="requirements"/> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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7 <expand macro="stdio"/> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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8 <expand macro="version_command"/> |
0 | 9 <command><![CDATA[ |
10 #if str( $reference_source.reference_source_selector ) == "history": | |
11 #set ref_fa = 'ref.fa' | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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12 ln -s '${reference_source.ref_fasta}' ref.fa && |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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13 samtools faidx ref.fa && |
0 | 14 #else: |
15 #set ref_fa = str( $reference_source.ref_fasta.fields.path ) | |
16 #end if | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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17 |
0 | 18 samtools calmd |
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e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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19 $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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20 #if str($option_set.option_sets) == 'advanced': |
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e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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21 $option_set.change_identical -C $option_set.adjust_mq |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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22 #end if |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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23 -b |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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24 '$input_bam' |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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25 '$ref_fa' |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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26 > '$calmd_output' |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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27 ]]></command> |
0 | 28 <inputs> |
1
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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29 <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" /> |
0 | 30 <conditional name="reference_source"> |
31 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
32 <option value="cached">Use a built-in genome</option> | |
33 <option value="history">Use a genome from the history</option> | |
34 </param> | |
35 <when value="cached"> | |
36 <param name="ref_fasta" type="select" label="Using reference genome"> | |
37 <options from_data_table="fasta_indexes"> | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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38 <filter type="data_meta" column="1" key="dbkey" ref="input_bam" /> |
0 | 39 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> |
40 </options> | |
41 </param> | |
42 </when> | |
43 <when value="history"> | |
44 <param name="ref_fasta" type="data" format="fasta" label="Using reference file" /> | |
45 </when> | |
46 </conditional> | |
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e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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47 <conditional name="baq_settings"> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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48 <param name="use_baq" argument="-r" type="select" |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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49 label="Do you also want BAQ (Base Alignment Quality) scores to be calculated?"> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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50 <option value="">No</option> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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51 <option value="-r">Yes, run BAQ calculation</option> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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52 </param> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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53 <when value=""> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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54 <param name="modify_quality" type="hidden" value="" /> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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55 <param name="extended_baq" type="hidden" value="" /> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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56 </when> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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57 <when value="-r"> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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58 <param name="modify_quality" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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59 label="Use BAQ to cap read base qualities" |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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60 help="By default, BAQ scores are stored in a separate BQ tag, and the read base quality string is left untouched. When you enable this option, the BAQ scores will be used directly to modify the quality string instead." /> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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61 <param name="extended_baq" argument="-E" type="boolean" truevalue="-E" falsevalue="" checked="false" label="Extended BAQ for better sensitivity" /> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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62 </when> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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63 </conditional> |
0 | 64 <conditional name="option_set"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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65 <param name="option_sets" type="select" label="Additional options"> |
0 | 66 <option value="default">Use defaults</option> |
67 <option value="advanced">Advanced options</option> | |
68 </param> | |
69 <when value="default" /> | |
70 <when value="advanced"> | |
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e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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71 <param name="change_identical" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="False" |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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72 label="Change identical bases to '='" |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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73 help="Replace bases in read sequences that match the reference base at that position with an equal sign" /> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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74 <param name="adjust_mq" argument="-C" type="integer" min="0" max="255" value="0" |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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75 label="Coefficient to cap mapping quality of poorly mapped reads" |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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76 help="Higher values for this setting mean a stronger downgrade of the mapping quality of reads with excessive mismatches (50: recommended setting for reads aligned with BWA, 0: do not downgrade mapping qualities)" /> |
0 | 77 </when> |
78 </conditional> | |
79 </inputs> | |
80 <outputs> | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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81 <data name="calmd_output" format="bam" label="${tool.name} on ${on_string}" /> |
0 | 82 </outputs> |
83 <tests> | |
84 <test> | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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85 <param name="use_baq" value="" /> |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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86 <param name="option_sets" value="default" /> |
0 | 87 <param name="input_bam" value="phiX.bam"/> |
88 <param name="reference_source_selector" value="history" /> | |
89 <param name="ref_fasta" value="phiX.fasta" /> | |
90 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" /> | |
91 </test> | |
92 <test> | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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93 <param name="use_baq" value="-r" /> |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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94 <param name="extended_baq" value="true" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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95 <param name="option_sets" value="advanced" /> |
0 | 96 <param name="change_identical" value="true" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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97 <param name="adjust_mq" value="50" /> |
0 | 98 <param name="input_bam" value="phiX.bam"/> |
99 <param name="reference_source_selector" value="history" /> | |
100 <param name="ref_fasta" value="phiX.fasta" /> | |
101 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" /> | |
102 </test> | |
103 </tests> | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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104 <help><![CDATA[ |
0 | 105 **What it does** |
106 | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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107 Generates the MD tag using the ``samtools calmd`` command. If the MD tag (see |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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108 SAM format reference below for explanation of SAM/BAM tags) is already present, |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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109 this command will give a warning if the MD tag generated is different from the |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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110 existing tag. |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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111 |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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112 Optionally, also generates the BQ tag to encode base alignment qualities, |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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113 caps the mapping quality of poorly mapping reads, and modifies read sequences |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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114 replacing bases matching the reference with ``=``. |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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115 |
e65c2cd0964c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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116 Outputs a BAM file. |
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118 ----- | |
119 | |
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120 **SAM/BAM tags written by this tool** |
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122 From the SAM format tag specification:: |
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124 MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7 | |
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125 NM (integer) Edit distance to the reference, including ambiguous bases but excluding clipping |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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126 BQ (string) String of offsets to base alignment quality (BAQ), of the same length as the read sequence. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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127 At the i-th read base, BAQ i = Q i − (BQ i − 64) where Q i is the i-th base quality. |
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129 See references for more information about SAM format tags. |
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130 ]]></help> |
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131 <expand macro="citations"/> |
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