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comparison picard_CollectInsertSizeMetrics.xml @ 0:5166ed57b1c4 draft

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Uploaded version 1.135
author avowinkel
date Mon, 06 Jul 2015 14:46:32 -0400
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1 <tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="1.135">
2 <description>plots distribution of insert sizes</description>
3 <macros>
4 <import>picard_macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="3.1.2">R</requirement>
8 </expand>
9 <command>
10 @java_options@
11 ##set up input files
12
13 #set $reference_fasta_filename = "localref.fa"
14
15 #if str( $reference_source.reference_source_selector ) == "history":
16 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
17 #else:
18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
19 #end if
20
21 java -jar \$JAVA_JAR_PATH/picard.jar
22 CollectInsertSizeMetrics
23 INPUT="${inputFile}"
24 OUTPUT="${outFile}"
25 HISTOGRAM_FILE="${histFile}"
26 DEVIATIONS="${deviations}"
27
28 #if str( $hist_width ):
29 HISTOGRAM_WIDTH="${hist_width}"
30 #end if
31
32 MINIMUM_PCT="${min_pct}"
33 REFERENCE_SEQUENCE="${reference_fasta_filename}"
34 ASSUME_SORTED="${assume_sorted}"
35 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
36
37 VALIDATION_STRINGENCY="${validation_stringency}"
38 QUIET=true
39 VERBOSITY=ERROR
40
41 </command>
42 <inputs>
43 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
44 <conditional name="reference_source">
45 <param name="reference_source_selector" type="select" label="Load reference genome from">
46 <option value="cached">Local cache</option>
47 <option value="history">History</option>
48 </param>
49 <when value="cached">
50 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
51 <options from_data_table="all_fasta">
52 </options>
53 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
54 </param>
55 </when>
56 <when value="history">
57 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
58 </when>
59 </conditional>
60 <param name="deviations" type="float" value="10.0" label="Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" help="DEVIATIONS; This option is offered because insert size data typically includes enough anomalous values from chimeras and other artifacts to make the mean and SD grossly misleading regarding the real distribution. default=10.0"/>
61 <param name="hist_width" type="integer" optional="True" label="Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail" help="HISTOGRAM_WIDTH; optional"/>
62 <param name="min_pct" type="float" value="0.05" label="When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" help="MINIMUM_PCT; (Range: 0 to 1). default=0.05. "/>
63 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
64 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
65 <option value="ALL_READS" selected="True">All reads</option>
66 <option value="SAMPLE">Sample</option>
67 <option value="LIBRARY">Library</option>
68 <option value="READ_GROUP">Read group</option>
69 </param>
70
71 <expand macro="VS" />
72
73 </inputs>
74
75 <outputs>
76 <data format="tabular" name="outFile"/>
77 <data format="pdf" name="histFile"/>
78 </outputs>
79
80 <tests>
81 <test>
82 <param name="metric_accumulation_level" value="ALL_READS"/>
83 <param name="deviations" value="10.0" />
84 <param name="hist_width" value="500" />
85 <param name="min_pct" value="0.05" />
86 <param name="assume_sorted" value="true" />
87 <param name="reference_source_selector" value="history" />
88 <param name="ref_file" value="picard_CollectInsertSizeMetrics_ref.fa" />
89 <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam" />
90 <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
91 </test>
92 </tests>
93
94 <stdio>
95 <exit_code range="1:" level="fatal"/>
96 </stdio>
97
98 <help>
99
100 .. class:: infomark
101
102 **Purpose**
103
104 Reads a SAM or BAM dataset and writes a file containing metrics about the statistical distribution of insert size (excluding duplicates) and generates a Histogram plot.
105
106 @dataset_collections@
107
108 @description@
109
110
111 DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN +
112 DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically
113 includes enough anomalous values from chimeras and other artifacts to make the mean and
114 sd grossly misleading regarding the real distribution. Default value: 10.0.
115
116 HISTOGRAM_WIDTH=Integer
117 W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail.
118 Also, when calculating mean and standard deviation, only bins &lt;= Histogram_WIDTH will be
119 included. Default value: not set.
120
121 MINIMUM_PCT=Float
122 M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that
123 have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05.
124
125 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
126 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
127 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
128
129 ASSUME_SORTED=Boolean
130 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default
131 value: true. This option can be set to 'null' to clear the default value. Possible
132 values: {true, false}
133
134 @more_info@
135
136 </help>
137 </tool>
138
139