Mercurial > repos > devteam > sam_pileup
diff sam_pileup.xml @ 0:95612c159681
Uploaded tool tarball.
| author | devteam |
|---|---|
| date | Mon, 26 Aug 2013 14:21:12 -0400 |
| parents | |
| children | e7d863c5c5d6 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam_pileup.xml Mon Aug 26 14:21:12 2013 -0400 @@ -0,0 +1,190 @@ +<tool id="sam_pileup" name="Generate pileup" version="1.1.1"> + <description>from BAM dataset</description> + <requirements> + <requirement type="package" version="0.1.16">samtools</requirement> + </requirements> + <command interpreter="python"> + sam_pileup.py + --input1=$input1 + --output=$output1 + --ref=$refOrHistory.reference + #if $refOrHistory.reference == "history": + --ownFile=$refOrHistory.ownFile + #else: + --ownFile="None" + #end if + --dbkey=${input1.metadata.dbkey} + --indexDir=${GALAXY_DATA_INDEX_DIR} + --bamIndex=${input1.metadata.bam_index} + --lastCol=$lastCol + --indels=$indels + --mapCap=$mapCap + --consensus=$c.consensus + #if $c.consensus == "yes": + --theta=$c.theta + --hapNum=$c.hapNum + --fraction=$c.fraction + --phredProb=$c.phredProb + #else: + --theta="None" + --hapNum="None" + --fraction="None" + --phredProb="None" + #end if + </command> + <inputs> + <conditional name="refOrHistory"> + <param name="reference" type="select" label="Will you select a reference genome from your history or use a built-in index?"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" /> + </param> + </when> + <when value="history"> + <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for" /> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" /> + </when> + </conditional> + <param name="lastCol" type="select" label="Whether or not to print the mapping quality as the last column" help="Makes the output easier to parse, but is space inefficient"> + <option value="no">Do not print the mapping quality as the last column</option> + <option value="yes">Print the mapping quality as the last column</option> + </param> + <param name="indels" type="select" label="Whether or not to print only output pileup lines containing indels"> + <option value="no">Print all lines</option> + <option value="yes">Print only lines containing indels</option> + </param> + <param name="mapCap" type="integer" value="60" label="Where to cap mapping quality" /> + <conditional name="c"> + <param name="consensus" type="select" label="Call consensus according to MAQ model?"> + <option selected="true" value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="theta" type="float" value="0.85" label="Theta parameter (error dependency coefficient) in the MAQ consensus calling model" /> + <param name="hapNum" type="integer" value="2" label="Number of haplotypes in the sample" help="Greater than or equal to 2" /> + <param name="fraction" type="float" value="0.001" label="Expected fraction of differences between a pair of haplotypes" /> + <param name="phredProb" type="integer" value="40" label="Phred probability of an indel in sequencing/prep" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="tabular" name="output1" label="${tool.name} on ${on_string}: converted pileup" /> + </outputs> + <tests> + <test> + <!-- + Bam to pileup command: + samtools faidx chr_m.fasta + samtools pileup -M 60 -f chr_m.fasta test-data/sam_pileup_in1.bam > sam_pileup_out1.pileup + chr_m.fasta is the prefix of the index + --> + <param name="reference" value="history" /> + <param name="input1" value="sam_pileup_in1.bam" ftype="bam" /> + <param name="ownFile" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" /> + <param name="lastCol" value="no" /> + <param name="indels" value="no" /> + <param name="mapCap" value="60" /> + <param name="consensus" value="no" /> + <output name="output1" file="sam_pileup_out1.pileup" /> + </test> + <test> + <!-- + Bam to pileup command: + samtools pileup -M 60 -c -T 0.85 -N 2 -r 0.001 -I 40 -f chr_m.fasta test-data/sam_pileup_in1.bam > sam_pileup_out2.pileup + chr_m.fasta is the prefix of the index + --> + <param name="reference" value="indexed" /> + <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" /> + <param name="lastCol" value="no" /> + <param name="indels" value="no" /> + <param name="mapCap" value="60" /> + <param name="consensus" value="yes" /> + <param name="theta" value="0.85" /> + <param name="hapNum" value="2" /> + <param name="fraction" value="0.001" /> + <param name="phredProb" value="40" /> + <output name="output1" file="sam_pileup_out2.pileup" /> + </test> + </tests> + <help> + +**What it does** + +Uses SAMTools_' pileup command to produce a pileup dataset from a provided BAM dataset. It generates two types of pileup datasets depending on the specified options. If *Call consensus according to MAQ model?* option is set to **No**, the tool produces simple pileup. If the option is set to **Yes**, a ten column pileup dataset with consensus is generated. Both types of datasets are briefly summarized below. + +.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml + +------ + +**Types of pileup datasets** + +The description of pileup format below is largely based on information that can be found on SAMTools Pileup_ documentation page. The 6- and 10-column variants are described below. + +.. _Pileup: http://samtools.sourceforge.net/pileup.shtml + +**Six column pileup**:: + + 1 2 3 4 5 6 + --------------------------------- + chrM 412 A 2 ., II + chrM 413 G 4 ..t, IIIH + chrM 414 C 4 ...a III2 + chrM 415 C 4 TTTt III7 + +where:: + + Column Definition + ------- ---------------------------- + 1 Chromosome + 2 Position (1-based) + 3 Reference base at that position + 4 Coverage (# reads aligning over that position) + 5 Bases within reads where (see Galaxy wiki for more info) + 6 Quality values (phred33 scale, see Galaxy wiki for more) + +**Ten column pileup** + +The `ten-column` (consensus_) pileup incorporates additional consensus information generated with *-c* option of *samtools pileup* command:: + + + 1 2 3 4 5 6 7 8 9 10 + ------------------------------------------------ + chrM 412 A A 75 0 25 2 ., II + chrM 413 G G 72 0 25 4 ..t, IIIH + chrM 414 C C 75 0 25 4 ...a III2 + chrM 415 C T 75 75 25 4 TTTt III7 + +where:: + + Column Definition + ------- -------------------------------------------------------- + 1 Chromosome + 2 Position (1-based) + 3 Reference base at that position + 4 Consensus bases + 5 Consensus quality + 6 SNP quality + 7 Maximum mapping quality + 8 Coverage (# reads aligning over that position) + 9 Bases within reads where (see Galaxy wiki for more info) + 10 Quality values (phred33 scale, see Galaxy wiki for more) + + +.. _consensus: http://samtools.sourceforge.net/cns0.shtml + +------ + +**Citation** + +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>`_ + + + </help> +</tool> + +