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88 lines
4.0 KiB
XML
88 lines
4.0 KiB
XML
<tool id="sam_pileup" name="SAM Pileup Format" version="1.0.0">
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<description>generates the pileup format for a provided BAM file</description>
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<command interpreter="python">
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sam_pileup.py
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--input1=$input1
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--output=$output1
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--ref=$refOrHistory.reference
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#if $refOrHistory.reference == "history":
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--ownFile=$refOrHistory.ownFile
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#else:
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--ownFile="None"
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#end if
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--dbkey=${input1.metadata.dbkey}
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--indexDir=${GALAXY_DATA_INDEX_DIR}
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--bamIndex=${input1.metadata.bam_index}
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--lastCol=$lastCol
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--indels=$indels
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--mapCap=$mapCap
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--consensus=$c.consensus
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#if $c.consensus == "yes":
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--theta=$c.theta
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--hapNum=$c.hapNum
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--fraction=$c.fraction
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--phredProb=$c.phredProb
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#else:
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--theta="None"
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--hapNum="None"
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--fraction="None"
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--phredProb="None"
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#end if
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</command>
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<inputs>
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<conditional name="refOrHistory">
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<param name="reference" type="select" label="Will you select a reference genome from your history or use a built-in index?">
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<option value="indexed">Use a built-in index</option>
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<option value="history">Use one from the history</option>
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</param>
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<when value="indexed">
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<param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for">
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<validator type="unspecified_build" />
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<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" />
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</param>
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</when>
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<when value="history">
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<param name="input1" type="data" format="sam, bam" label="Select the BAM file to generate the pileup file for" />
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<param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" />
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</when>
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</conditional>
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<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">
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<option value="no">Do not print the mapping quality as the last column</option>
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<option value="yes">Print the mapping quality as the last column</option>
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</param>
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<param name="indels" type="select" label="Whether or not to print only output pileup lines containing indels">
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<option value="no">Print all lines</option>
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<option value="yes">Print only lines containing indels</option>
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</param>
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<param name="mapCap" type="integer" value="60" label="Where to cap mapping quality" />
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<conditional name="c">
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<param name="consensus" type="select" label="Whether or not to call the consensus sequence using the MAQ consensus model">
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<option value="no">Don't use MAQ consensus model</option>
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<option value="yes">Use the MAQ consensus model</option>
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</param>
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<when value="no" />
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<when value="yes">
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<param name="theta" type="float" value="0.85" label="Theta paramter (error dependency coefficient) in the MAQ consensus calling model" />
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<param name="hapNum" type="integer" value="2" label="Number of haplotypes in the sample" help="Greater than or equal to 2" />
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<param name="fraction" type="float" value="0.001" label="Expected fraction of differences between a pair of haplotypes" />
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<param name="phredProb" type="integer" value="40" label="Phred probability of an indel in sequencing/prep" />
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</when>
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</conditional>
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</inputs>
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<outputs>
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<data format="tabular" name="output1" />
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</outputs>
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<!-- tests are not possible because bam is a non-sniffable binary format and cannot be uploaded without being corrupted -->
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<help>
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**What it does**
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Uses SAMTools_' pileup command to produce a file in the pileup format based on the provided BAM file.
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.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
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</help>
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</tool>
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