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comparison rgPicardInsertSize.xml @ 0:1cd7f3b42609

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Uploaded tool.
author devteam
date Tue, 23 Oct 2012 13:14:29 -0400
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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">
5 picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations"
6 --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel"
7 -j "\$JAVA_JAR_PATH/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file"
8 </command>
9 <inputs>
10 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for"
11 help="If empty, upload or import a SAM/BAM dataset."/>
12 <param name="out_prefix" value="Insertion size metrics" type="text"
13 label="Title for the output file" help="Use this remind you what the job was for" size="120" />
14 <param name="deviations" value="10.0" type="float"
15 label="Deviations" size="5"
16 help="See Picard documentation: Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" />
17 <param name="histWidth" value="0" type="integer"
18 label="Histogram width" size="5"
19 help="Explicitly sets the histogram width option - leave 0 to ignore" />
20 <param name="minPct" value="0.05" type="float"
21 label="Minimum percentage" size="5"
22 help="Discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" />
23 <param name="malevel" value="0" type="select" multiple="true" label="Metric Accumulation Level"
24 help="Level(s) at which metrics will be accumulated">
25 <option value="ALL_READS" selected="true">All reads (default)</option>
26 <option value="SAMPLE" default="true">Sample</option>
27 <option value="LIBRARY" default="true">Library</option>
28 <option value="READ_GROUP" default="true">Read group</option>
29 </param>
30 </inputs>
31 <outputs>
32 <data format="html" name="html_file" label="InsertSize_${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>