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Nicola Soranzo
f865e8359f
Also: - dos2unix test/functional/tools/for_workflows/head.xml - Single-quote text and data params in `<command/>` - Remove deprecated `interpreter` attribute of `<command />`
114 lines
4.6 KiB
XML
114 lines
4.6 KiB
XML
<tool id="maq_cs_wrapper" name="MAQ for SOLiD" version="1.0.0">
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<description> </description>
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<command>
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python '$__tool_directory__/maq_cs_wrapper.py'
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'$output1'
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'$output2'
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'$ref'
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'$library_type.f3_reads'
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'$library_type.f3_qual'
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$library_type.is_paired
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#if $library_type.is_paired == "yes":
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'$library_type.r3_reads'
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'$library_type.r3_qual'
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#else:
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"None"
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"None"
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#end if
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$min_mapqual
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$max_mismatch
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'$output3'
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</command>
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<inputs>
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<param name="ref" type="data" format="fasta" label="Target Genome"/>
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<conditional name="library_type">
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<param name="is_paired" type="select" label="Is the library mate-paired?" multiple="false">
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<when value="no">
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<param name="f3_reads" type="data" format="csfasta" label="F3 reads file"/>
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<param name="f3_qual" type="data" format="qualsolid" 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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</when>
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<when value="yes">
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<param name="f3_reads" type="data" format="csfasta" label="F3 reads file"/>
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<param name="f3_qual" type="data" format="qualsolid" 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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<param name="r3_reads" type="data" format="csfasta" label="R3 reads file"/>
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<param name="r3_qual" type="data" format="qualsolid" 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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</when>
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</conditional>
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<param name="min_mapqual" type="integer" 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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<param name="max_mismatch" type="integer" 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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</inputs>
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<outputs>
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<data name="output1" format="tabular" metadata_source="ref" />
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<data name="output2" format="tabular" metadata_source="ref" />
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<data name="output3" format="customtrack" metadata_source="ref" />
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</outputs>
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<!-- "ToolTestCase does not deal with multiple outputs properly yet."
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<tests>
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<test>
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<param name="ref" value="phiX_mod.fasta" />
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<param name="is_paired" value="no" />
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<param name="f3_reads" value="phiX_solid.csfasta" />
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<param name="f3_qual" value="phiX_solid.qualsolid" />
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<param name="min_mapqual" value="0" />
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<param name="max_mismatch" value="7" />
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<output name="output1" file="phiX_solid_maq.map" />
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<output name="output2" file="phiX_solid_maq.pileup" />
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<output name="output3" file="phiX_solid_maq.ctrack" />
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</test>
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</tests>
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-->
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<help>
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.. class:: infomark
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**What it does**
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This tool maps SOLiD color-space reads against the target genome using MAQ. It produces three output datasets:
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**ALIGNMENT INFO** : contains the read alignment information,
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**PILEUP** : contains the coverage and SNP statistics for every nucleotide of the target genome,
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**CUSTOM TRACK** : contains the coverage and SNP statistics as custom tracks displayable in the UCSC browser.
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-----
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**The ALIGNMENT INFO dataset will contain the following fields:**
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* column 1 = read name
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* column 2 = chromosome
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* column 3 = position
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* column 4 = strand
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* column 5 = insert size from the outer coorniates of a pair
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* column 6 = paired flag
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* column 7 = mapping quality
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* column 8 = single-end mapping quality
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* column 9 = alternative mapping quality
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* column 10 = number of mismatches of the best hit
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* column 11 = sum of qualities of mismatched bases of the best hit
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* column 12 = number of 0-mismatch hits of the first 24bp
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* column 13 = number of 1-mismatch hits of the first 24bp on the reference
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* column 14 = length of the read
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* column 15 = read sequence
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* column 16 = read quality
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**The PILEUP dataset will contain the following fields:**
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* column 1 = chromosome
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* column 2 = position
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* column 3 = reference nucleotide
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* column 4 = coverage (number of reads that cover this position)
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* column 5 = number of SNPs
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* column 6 = number of As
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* column 7 = number of Ts
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* column 8 = number of Gs
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* column 9 = number of Cs
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</help>
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<code file="maq_cs_wrapper_code.py"/>
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</tool>
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