[2] | 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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