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view picard_InsertSizeMetrics.xml @ 135:1790970e47fe draft
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author | devteam |
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date | Wed, 26 Feb 2014 17:29:45 -0500 |
parents | 7ea806787cf6 |
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<tool name="Insertion size metrics" id="PicardInsertSize" version="1.106.0"> <description>for PAIRED data</description> <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements> <command interpreter="python"> picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" --deviations "${deviations}" --histwidth "${histWidth}" --minpct "${minPct}" --malevel "${malevel}" -j "\$JAVA_JAR_PATH/CollectInsertSizeMetrics.jar" -d "${html_file.files_path}" -t "${html_file}" </command> <inputs> <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for" help="If empty, upload or import a SAM/BAM dataset."/> <param name="out_prefix" value="Insertion size metrics" type="text" label="Title for the output file" help="Use this remind you what the job was for" size="120" /> <param name="deviations" value="10.0" type="float" label="Deviations" size="5" help="See Picard documentation: Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" /> <param name="histWidth" value="0" type="integer" label="Histogram width" size="5" help="Explicitly sets the histogram width option - leave 0 to ignore" /> <param name="minPct" value="0.05" type="float" label="Minimum percentage" size="5" help="Discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" /> <param name="malevel" value="0" type="select" multiple="true" label="Metric Accumulation Level" help="Level(s) at which metrics will be accumulated"> <option value="ALL_READS" selected="true">All reads (default)</option> <option value="SAMPLE" default="true">Sample</option> <option value="LIBRARY" default="true">Library</option> <option value="READ_GROUP" default="true">Read group</option> </param> </inputs> <outputs> <data format="html" name="html_file" label="InsertSize_${out_prefix}.html"/> </outputs> <tests> <test> <param name="input_file" value="picard_input_tiny.sam" /> <param name="out_prefix" value="Insertion size metrics" /> <param name="deviations" value="10.0" /> <param name="histWidth" value="0" /> <param name="minPct" value="0.01" /> <param name="malevel" value="ALL_READS" /> <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" compare="contains" lines_diff="40" /> </test> </tests> <help> .. class:: infomark **Purpose** Reads a SAM or BAM file and describes the distribution of insert size (excluding duplicates) with metrics and a histogram plot. **Picard documentation** This is a Galaxy wrapper for CollectInsertSizeMetrics, a part of the external package Picard-tools_. .. _Picard-tools: http://www.google.com/search?q=picard+samtools .. class:: warningmark **Useful for paired data only** This tool works for paired data only and can be expected to fail for single end data. ----- .. class:: infomark **Inputs, outputs, and parameters** Picard documentation says (reformatted for Galaxy): .. csv-table:: :header-rows: 1 Option,Description "INPUT=File","SAM or BAM file Required." "OUTPUT=File","File to write insert size metrics to Required." "HISTOGRAM_FILE=File","File to write insert size histogram chart to Required." "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." "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. " "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." "STOP_AFTER=Integer","Stop after processing N reads, mainly for debugging. Default value: 0." "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false." .. class:: warningmark **Warning on SAM/BAM quality** 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** flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears to be the only way to deal with SAM/BAM that cannot be parsed. </help> </tool>