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1 <tool id="samtools_calmd" name="CalMD" version="2.0">
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2 <description>recalculate MD/NM tags</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"></expand>
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7 <expand macro="stdio"></expand>
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8 <expand macro="version_command"></expand>
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9 <command><![CDATA[
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10 #if str( $reference_source.reference_source_selector ) == "history":
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11 #set ref_fa = 'ref.fa'
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12 ln -s "${reference_source.ref_fasta}" ref.fa && samtools faidx ref.fa &&
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13 #else:
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14 #set ref_fa = str( $reference_source.ref_fasta.fields.path )
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15 #end if
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16 samtools calmd
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17 #if str($option_set.option_sets) == 'advanced':
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18 $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq
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19 #end if
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20 -b "$input_bam" "$ref_fa" > "$calmd_output" ]]>
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21 </command>
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22 <inputs>
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23 <param format="bam" name="input_bam" type="data" label="BAM file to recalculate" />
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24 <conditional name="reference_source">
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25 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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26 <option value="cached">Use a built-in genome</option>
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27 <option value="history">Use a genome from the history</option>
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28 </param>
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29 <when value="cached">
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30 <param name="ref_fasta" type="select" label="Using reference genome">
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31 <options from_data_table="fasta_indexes">
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32 <filter type="data_meta" column="0" key="dbkey" ref="input_bam" />
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33 <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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34 </options>
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35 </param>
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36 </when>
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37 <when value="history">
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38 <param name="ref_fasta" type="data" format="fasta" label="Using reference file" />
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39 </when>
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40 </conditional>
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41 <conditional name="option_set">
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42 <param name="option_sets" type="select" label="Options">
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43 <option value="default">Use defaults</option>
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44 <option value="advanced">Advanced options</option>
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45 </param>
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46 <when value="default" />
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47 <when value="advanced">
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48 <param name="change_identical" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" help="-e"/>
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49 <param name="modify_quality" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" help="-A"/>
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50 <param name="compute_cap" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" help="-r"/>
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51 <param name="extended_baq" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" help="-E"/>
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52 </when>
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53 </conditional>
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54 </inputs>
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55 <outputs>
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56 <data format="bam" name="calmd_output" label="${tool.name} on ${on_string}" />
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="option_sets" value="default" />
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61 <param name="input_bam" value="phiX.bam"/>
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62 <param name="reference_source_selector" value="history" />
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63 <param name="ref_fasta" value="phiX.fasta" />
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64 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
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65 </test>
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66 <test>
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67 <param name="option_sets" value="advanced" />
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68 <param name="change_identical" value="true" />
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69 <param name="extended_baq" value="true" />
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70 <param name="input_bam" value="phiX.bam"/>
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71 <param name="reference_source_selector" value="history" />
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72 <param name="ref_fasta" value="phiX.fasta" />
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73 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
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74 </test>
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75 </tests>
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76 <help>
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77 **What it does**
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78
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79 Generates the MD tag using ``samtools calmd`` command. If the MD tag (see SAM format refernce below for explanation of SAM/BAM tags) is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file. The command has the following options::
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80
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81 -e change identical bases to '='
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82 -A modify the quality string
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83 -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)
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84 -E extended BAQ for better sensitivity but lower specificity
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85
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86 -----
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87
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88 **NM and MD tags**
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89
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90 From SAM format specification::
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91
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92 MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7
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93 NM (indeger) Edit distance to the reference, including ambiguous bases but excluding clipping
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94
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95 See refernces for more information about SAM format tags.
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96
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97 </help>
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98 <expand macro="citations"></expand>
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99 </tool>
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