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1 <tool id="samtools_calmd" name="Recalculate" version="1.0.0">
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2 <description>MD/NM tags and '=' bases</description>
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3 <requirements>
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4 <requirement type="package" version="1.1">samtools</requirement>
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5 </requirements>
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6 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
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7 <command><![CDATA[
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8 #if str( $reference_source.reference_source_selector ) == "history":
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9 #set ref_fa = 'ref.fa'
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10 ln -s "${reference_source.ref_fasta}" ref.fa && samtools faidx ref.fa &&
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11 #else:
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12 #set ref_fa = str( $reference_source.ref_fasta.fields.path )
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13 #end if
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14 samtools calmd
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15 #if str($option_set.option_sets) == 'advanced':
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16 $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq
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17 #end if
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18 -b "$input_bam" "$ref_fa" > "$calmd_output" ]]>
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19 </command>
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20 <stdio>
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21 <exit_code range="1:" level="fatal" description="Error" />
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22 </stdio>
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23 <inputs>
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24 <param format="bam" name="input_bam" type="data" label="BAM file to recalculate" />
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25 <conditional name="reference_source">
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26 <param name="reference_source_selector" type="select" label="Choose the source for the reference FASTA">
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27 <option value="cached">Locally cached</option>
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28 <option value="history">History</option>
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29 </param>
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30 <when value="cached">
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31 <param name="ref_fasta" type="select" label="Using reference genome">
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32 <options from_data_table="fasta_indexes">
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33 <filter type="data_meta" column="0" key="dbkey" ref="input_bam" />
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34 <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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35 </options>
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36 </param>
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37 </when>
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38 <when value="history">
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39 <param name="ref_fasta" type="data" format="fasta" label="Using reference file" />
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40 </when>
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41 </conditional>
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42 <conditional name="option_set">
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43 <param name="option_sets" type="select" label="Options">
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44 <option value="default">Use defaults</option>
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45 <option value="advanced">Advanced options</option>
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46 </param>
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47 <when value="default" />
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48 <when value="advanced">
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49 <param name="change_identical" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" />
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50 <param name="modify_quality" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" />
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51 <param name="compute_cap" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" />
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52 <param name="extended_baq" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" />
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53 </when>
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54 </conditional>
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55 </inputs>
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56 <outputs>
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57 <data format="bam" name="calmd_output" label="${tool.name} on ${on_string}" />
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param name="option_sets" value="default" />
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62 <param name="input_bam" value="phiX.bam" dbkey="phiX" />
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63 <param name="reference_source|reference_source_selector" value="history" />
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64 <param name="ref_fasta" value="phiX.fasta" dbkey="phiX" />
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65 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
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66 </test>
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67 <!-- Using the test-data-repo's phiX.fa should produce the same output. -->
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68 <test>
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69 <param name="option_sets" value="default" />
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70 <param name="input_bam" value="phiX.bam" dbkey="phiX" />
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71 <param name="reference_source|reference_source_selector" value="cached" />
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72 <param name="ref_fasta" value="phiX" />
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73 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
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74 </test>
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75 <test>
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76 <param name="option_sets" value="advanced" />
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77 <param name="change_identical" value="true" />
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78 <param name="extended_baq" value="true" />
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79 <param name="input_bam" value="phiX.bam" dbkey="phiX" />
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80 <param name="reference_source|reference_source_selector" value="history" />
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81 <param name="ref_fasta" value="phiX.fasta" dbkey="phiX" />
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82 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
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83 </test>
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84 <!-- Using the test-data-repo's phiX.fa should, as before, produce the same output. -->
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85 <test>
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86 <param name="option_sets" value="advanced" />
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87 <param name="change_identical" value="true" />
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88 <param name="extended_baq" value="true" />
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89 <param name="input_bam" value="phiX.bam" dbkey="phiX" />
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90 <param name="reference_source|reference_source_selector" value="cached" />
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91 <param name="ref_fasta" value="phiX" />
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92 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
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93 </test>
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94 </tests>
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95 <help>
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96 **What it does**
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97
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98 Generate the MD tag. If the MD tag is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file.
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99
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100 ------
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101
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102 **Citation**
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103
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104 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
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105
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106
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107 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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108
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109 </help>
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110 </tool>
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