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98 lines
4.6 KiB
XML
98 lines
4.6 KiB
XML
<tool name="Insertion size metrics" id="PicardInsertSize" version="1.56.0">
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<description>for PAIRED data</description>
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<requirements><requirement type="package">picard</requirement></requirements>
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<command interpreter="python">
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picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations"
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--histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel"
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-j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file"
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</command>
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<inputs>
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<param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for"
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help="If empty, upload or import a SAM/BAM dataset."/>
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<param name="out_prefix" value="Insertion size metrics" type="text"
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label="Title for the output file" help="Use this remind you what the job was for" size="120" />
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<param name="deviations" value="10.0" type="float"
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label="Deviations" size="5"
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help="See Picard documentation: Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" />
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<param name="histWidth" value="0" type="integer"
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label="Histogram width" size="5"
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help="Explicitly sets the histogram width option - leave 0 to ignore" />
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<param name="minPct" value="0.05" type="float"
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label="Minimum percentage" size="5"
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help="Discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" />
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<param name="malevel" value="0" type="select" multiple="true" label="Metric Accumulation Level"
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help="Level(s) at which metrics will be accumulated">
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<option value="ALL_READS" selected="true">All reads (default)</option>
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<option value="SAMPLE" default="true">Sample</option>
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<option value="LIBRARY" default="true">Library</option>
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<option value="READ_GROUP" default="true">Read group</option>
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</param>
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</inputs>
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<outputs>
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<data format="html" name="html_file" label="InsertSize_${out_prefix}.html"/>
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</outputs>
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<tests>
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<test>
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<param name="input_file" value="picard_input_tiny.sam" />
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<param name="out_prefix" value="Insertion size metrics" />
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<param name="deviations" value="10.0" />
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<param name="histWidth" value="0" />
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<param name="minPct" value="0.01" />
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<param name="malevel" value="ALL_READS" />
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<output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" compare="contains" lines_diff="40" />
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</test>
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</tests>
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<help>
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.. class:: infomark
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**Purpose**
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Reads a SAM or BAM file and describes the distribution
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of insert size (excluding duplicates) with metrics and a histogram plot.
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**Picard documentation**
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This is a Galaxy wrapper for CollectInsertSizeMetrics, a part of the external package Picard-tools_.
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.. _Picard-tools: http://www.google.com/search?q=picard+samtools
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.. class:: warningmark
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**Useful for paired data only**
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This tool works for paired data only and can be expected to fail for single end data.
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-----
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.. class:: infomark
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**Inputs, outputs, and parameters**
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Picard documentation says (reformatted for Galaxy):
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.. csv-table::
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:header-rows: 1
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Option,Description
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"INPUT=File","SAM or BAM file Required."
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"OUTPUT=File","File to write insert size metrics to Required."
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"HISTOGRAM_FILE=File","File to write insert size histogram chart to Required."
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"TAIL_LIMIT=Integer","When calculating mean and stdev stop when the bins in the tail of the distribution contain fewer than mode/TAIL_LIMIT items. This also limits how much data goes into each data category of the histogram."
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"HISTOGRAM_WIDTH=Integer","Explicitly sets the histogram width, overriding the TAIL_LIMIT option. Also, when calculating mean and stdev, only bins LE HISTOGRAM_WIDTH will be included. "
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"MINIMUM_PCT=Float","When generating the histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads. (Range: 0 to 1) Default value: 0.01."
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"STOP_AFTER=Integer","Stop after processing N reads, mainly for debugging. Default value: 0."
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"CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false."
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.. class:: warningmark
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**Warning on SAM/BAM quality**
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Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
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flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
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to be the only way to deal with SAM/BAM that cannot be parsed.
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</help>
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</tool>
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