Mercurial > repos > devteam > picard
annotate rgPicardInsertSize.xml @ 3:bf1c3f9f8282
Fix for FastqToSam MAX_Q usage detection.
| author | Daniel Blankenberg <dan@bx.psu.edu> |
|---|---|
| date | Fri, 03 May 2013 17:13:01 -0400 |
| parents | 9227b8c3093b |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool name="Insertion size metrics" id="PicardInsertSize" version="1.56.0"> |
| 2 <description>for PAIRED data</description> | |
| 3 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> | |
| 4 <command interpreter="python"> | |
|
2
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
5 picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" --deviations "${deviations}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
6 --histwidth "${histWidth}" --minpct "${minPct}" --malevel "${malevel}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
7 -j "\$JAVA_JAR_PATH/CollectInsertSizeMetrics.jar" -d "${html_file.files_path}" -t "${html_file}" |
| 0 | 8 </command> |
| 9 <inputs> | |
| 10 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for" | |
| 11 help="If empty, upload or import a SAM/BAM dataset."/> | |
| 12 <param name="out_prefix" value="Insertion size metrics" type="text" | |
| 13 label="Title for the output file" help="Use this remind you what the job was for" size="120" /> | |
| 14 <param name="deviations" value="10.0" type="float" | |
| 15 label="Deviations" size="5" | |
| 16 help="See Picard documentation: Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" /> | |
| 17 <param name="histWidth" value="0" type="integer" | |
| 18 label="Histogram width" size="5" | |
| 19 help="Explicitly sets the histogram width option - leave 0 to ignore" /> | |
| 20 <param name="minPct" value="0.05" type="float" | |
| 21 label="Minimum percentage" size="5" | |
| 22 help="Discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" /> | |
| 23 <param name="malevel" value="0" type="select" multiple="true" label="Metric Accumulation Level" | |
| 24 help="Level(s) at which metrics will be accumulated"> | |
| 25 <option value="ALL_READS" selected="true">All reads (default)</option> | |
| 26 <option value="SAMPLE" default="true">Sample</option> | |
| 27 <option value="LIBRARY" default="true">Library</option> | |
| 28 <option value="READ_GROUP" default="true">Read group</option> | |
| 29 </param> | |
| 30 </inputs> | |
| 31 <outputs> | |
| 32 <data format="html" name="html_file" label="InsertSize_${out_prefix}.html"/> | |
| 33 </outputs> | |
| 34 <tests> | |
| 35 <test> | |
| 36 <param name="input_file" value="picard_input_tiny.sam" /> | |
| 37 <param name="out_prefix" value="Insertion size metrics" /> | |
| 38 <param name="deviations" value="10.0" /> | |
| 39 <param name="histWidth" value="0" /> | |
| 40 <param name="minPct" value="0.01" /> | |
| 41 <param name="malevel" value="ALL_READS" /> | |
| 42 <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" compare="contains" lines_diff="40" /> | |
| 43 </test> | |
| 44 </tests> | |
| 45 <help> | |
| 46 | |
| 47 | |
| 48 .. class:: infomark | |
| 49 | |
| 50 **Purpose** | |
| 51 | |
| 52 Reads a SAM or BAM file and describes the distribution | |
| 53 of insert size (excluding duplicates) with metrics and a histogram plot. | |
| 54 | |
| 55 **Picard documentation** | |
| 56 | |
| 57 This is a Galaxy wrapper for CollectInsertSizeMetrics, a part of the external package Picard-tools_. | |
| 58 | |
| 59 .. _Picard-tools: http://www.google.com/search?q=picard+samtools | |
| 60 | |
| 61 .. class:: warningmark | |
| 62 | |
| 63 **Useful for paired data only** | |
| 64 | |
| 65 This tool works for paired data only and can be expected to fail for single end data. | |
| 66 | |
| 67 ----- | |
| 68 | |
| 69 .. class:: infomark | |
| 70 | |
| 71 **Inputs, outputs, and parameters** | |
| 72 | |
| 73 Picard documentation says (reformatted for Galaxy): | |
| 74 | |
| 75 .. csv-table:: | |
| 76 :header-rows: 1 | |
| 77 | |
| 78 Option,Description | |
| 79 "INPUT=File","SAM or BAM file Required." | |
| 80 "OUTPUT=File","File to write insert size metrics to Required." | |
| 81 "HISTOGRAM_FILE=File","File to write insert size histogram chart to Required." | |
| 82 "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." | |
| 83 "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. " | |
| 84 "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." | |
| 85 "STOP_AFTER=Integer","Stop after processing N reads, mainly for debugging. Default value: 0." | |
| 86 "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false." | |
| 87 | |
| 88 .. class:: warningmark | |
| 89 | |
| 90 **Warning on SAM/BAM quality** | |
| 91 | |
| 92 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** | |
| 93 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears | |
| 94 to be the only way to deal with SAM/BAM that cannot be parsed. | |
| 95 | |
| 96 </help> | |
| 97 </tool> |