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1 <tool id="maq_cs_wrapper" name="MAQ for SOLiD" version="1.0.0">
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2 <description> </description>
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3 <command interpreter="python">
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4 maq_cs_wrapper.py
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5 $output1
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6 $output2
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7 $ref
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8 $library_type.f3_reads
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9 $library_type.f3_qual
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10 $library_type.is_paired
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11 #if $library_type.is_paired == "yes":
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12 $library_type.r3_reads
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13 $library_type.r3_qual
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14 #else:
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15 "None"
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16 "None"
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17 #end if
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18 $min_mapqual
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19 $max_mismatch
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20 $output3
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21
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22 </command>
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23
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24 <inputs>
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25 <param name="ref" type="data" format="fasta" label="Target Genome"/>
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26 <conditional name="library_type">
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27 <param name="is_paired" type="select" label="Is the library mate-paired?" multiple="false">
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28 <option value="no">No</option>
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29 <option value="yes">Yes</option>
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30 </param>
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31 <when value="no">
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32 <param name="f3_reads" type="data" format="csfasta" label="F3 reads file"/>
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33 <param format="qualsolid" name="f3_qual" type="data" label="F3 quality file" help="If your dataset doesn't show up in the menu, click the pencil icon next to your dataset and set the datatype to 'qualsolid'" />
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34 </when>
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35 <when value="yes">
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36 <param name="f3_reads" type="data" format="csfasta" label="F3 reads file"/>
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37 <param format="qualsolid" name="f3_qual" type="data" label="F3 quality file" help="If your dataset doesn't show up in the menu, click the pencil icon next to your dataset and set the datatype to 'qualsolid'" />
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38 <param name="r3_reads" type="data" format="csfasta" label="R3 reads file"/>
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39 <param format="qualsolid" name="r3_qual" type="data" label="R3 quality file" help="If your dataset doesn't show up in the menu, click the pencil icon next to your dataset and set the datatype to 'qualsolid'" />
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40 </when>
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41 </conditional>
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42 <param name="min_mapqual" type="integer" size="3" value="0" label="Minimum mapping quality allowed for a read to be used" help="Reads below the specified mapping quality will not be considered in coverage and SNP analysis."/>
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43 <param name="max_mismatch" type="integer" size="3" value="7" label="Maximum number of mismatches allowed for a read to be used" help="Reads above the specified threshold will not be considered in coverage and SNP analysis."/>
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44 </inputs>
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45 <outputs>
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46 <data format="tabular" name="output1" metadata_source="ref" />
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47 <data format="tabular" name="output2" metadata_source="ref" />
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48 <data format="customtrack" name="output3" metadata_source="ref" />
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49 </outputs>
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50
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51 <!-- "ToolTestCase does not deal with multiple outputs properly yet."
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52 <tests>
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53
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54 <test>
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55 <param name="ref" value="phiX_mod.fasta" />
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56 <param name="is_paired" value="no" />
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57 <param name="f3_reads" value="phiX_solid.csfasta" />
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58 <param name="f3_qual" value="phiX_solid.qualsolid" />
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59 <param name="min_mapqual" value="0" />
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60 <param name="max_mismatch" value="7" />
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61 <output name="output1" file="phiX_solid_maq.map" />
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62 <output name="output2" file="phiX_solid_maq.pileup" />
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63 <output name="output3" file="phiX_solid_maq.ctrack" />
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64
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65 </test>
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66 </tests>
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67 -->
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68 <help>
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69
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70 .. class:: infomark
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71
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72 **What it does**
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73
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74 This tool maps SOLiD color-space reads against the target genome using MAQ. It produces three output datasets:
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75
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76
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77 **ALIGNMENT INFO** : contains the read alignment information,
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78
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79 **PILEUP** : contains the coverage and SNP statistics for every nucleotide of the target genome,
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80
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81 **CUSTOM TRACK** : contains the coverage and SNP statistics as custom tracks displayable in the UCSC browser.
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82
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83 -----
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84
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85 **The ALIGNMENT INFO dataset will contain the following fields:**
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86
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87 * column 1 = read name
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88 * column 2 = chromosome
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89 * column 3 = position
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90 * column 4 = strand
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91 * column 5 = insert size from the outer coorniates of a pair
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92 * column 6 = paired flag
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93 * column 7 = mapping quality
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94 * column 8 = single-end mapping quality
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95 * column 9 = alternative mapping quality
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96 * column 10 = number of mismatches of the best hit
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97 * column 11 = sum of qualities of mismatched bases of the best hit
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98 * column 12 = number of 0-mismatch hits of the first 24bp
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99 * column 13 = number of 1-mismatch hits of the first 24bp on the reference
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100 * column 14 = length of the read
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101 * column 15 = read sequence
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102 * column 16 = read quality
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103
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104
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105 **The PILEUP dataset will contain the following fields:**
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106
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107 * column 1 = chromosome
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108 * column 2 = position
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109 * column 3 = reference nucleotide
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110 * column 4 = coverage (number of reads that cover this position)
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111 * column 5 = number of SNPs
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112 * column 6 = number of As
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113 * column 7 = number of Ts
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114 * column 8 = number of Gs
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115 * column 9 = number of Cs
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116
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117 </help>
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118 <code file="maq_cs_wrapper_code.py"/>
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119
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120 </tool>
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