picard: picard_CollectInsertSizeMetrics.xml annotate

annotate picard_CollectInsertSizeMetrics.xml @ 16:6741a8ace658 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

author	iuc
date	Wed, 08 Feb 2017 12:45:35 -0500
parents	465cbb0cf2eb
children	5053a18d9bc8

rev	line source
8 3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	1 <tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="@TOOL_VERSION@.0">
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	2 <description>plots distribution of insert sizes</description>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	3 <macros>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	4 <import>picard_macros.xml</import>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	5 </macros>
8 3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	6 <expand macro="requirements">
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	7 <requirement type="package" version="3.3.1">r</requirement>
8 3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	8 </expand>
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	9 <command detect_errors="exit_code"><![CDATA[
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	10 @java_options@
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	11 @symlink_element_identifier@
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	12 ##set up input files
3d4f1fa26f0e Uploaded devteam parents: diff changeset	13
3d4f1fa26f0e Uploaded devteam parents: diff changeset	14 #set $reference_fasta_filename = "localref.fa"
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	15
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	16 #if str( $reference_source.reference_source_selector ) == "history":
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	17 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	18 #else:
3d4f1fa26f0e Uploaded devteam parents: diff changeset	19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
3d4f1fa26f0e Uploaded devteam parents: diff changeset	20 #end if
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	21
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	22 picard
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	23 CollectInsertSizeMetrics
14 465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f devteam parents: 13 diff changeset	24 INPUT='$escaped_element_identifier'
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	25 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	26 HISTOGRAM_FILE="${histFile}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	27 DEVIATIONS="${deviations}"
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	28
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	29 #if str( $hist_width ):
3d4f1fa26f0e Uploaded devteam parents: diff changeset	30 HISTOGRAM_WIDTH="${hist_width}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	31 #end if
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	32
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	33 MINIMUM_PCT="${min_pct}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	34 REFERENCE_SEQUENCE="${reference_fasta_filename}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	35 ASSUME_SORTED="${assume_sorted}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	36 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	37
3d4f1fa26f0e Uploaded devteam parents: diff changeset	38 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	39 QUIET=true
3d4f1fa26f0e Uploaded devteam parents: diff changeset	40 VERBOSITY=ERROR
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	41
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	42 ]]></command>
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	43 <inputs>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	44 <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."/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	45 <conditional name="reference_source">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	46 <param name="reference_source_selector" type="select" label="Load reference genome from">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	47 <option value="cached">Local cache</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	48 <option value="history">History</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	49 </param>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	50 <when value="cached">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	51 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	52 <options from_data_table="all_fasta">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	53 </options>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	54 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	55 </param>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	56 </when>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	57 <when value="history">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	58 <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" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	59 </when>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	60 </conditional>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	61 <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"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	62 <param name="hist_width" type="integer" optional="True" label="Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail" help="HISTOGRAM_WIDTH; optional"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	63 <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. "/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	64 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	65 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	66 <option value="ALL_READS" selected="True">All reads</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	67 <option value="SAMPLE">Sample</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	68 <option value="LIBRARY">Library</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	69 <option value="READ_GROUP">Read group</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	70 </param>
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	71
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	72 <expand macro="VS" />
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	73
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	74 </inputs>
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	75
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	76 <outputs>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	77 <data format="tabular" name="outFile"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	78 <data format="pdf" name="histFile"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	79 </outputs>
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	80
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	81 <tests>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	82 <test>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	83 <param name="metric_accumulation_level" value="ALL_READS"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	84 <param name="deviations" value="10.0" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	85 <param name="hist_width" value="500" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	86 <param name="min_pct" value="0.05" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	87 <param name="assume_sorted" value="true" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	88 <param name="reference_source_selector" value="history" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	89 <param name="ref_file" value="picard_CollectInsertSizeMetrics_ref.fa" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	90 <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	91 <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	92 </test>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	93 </tests>
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	94
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	95
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	96 <help>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	97
3d4f1fa26f0e Uploaded devteam parents: diff changeset	98 .. class:: infomark
3d4f1fa26f0e Uploaded devteam parents: diff changeset	99
3d4f1fa26f0e Uploaded devteam parents: diff changeset	100 Purpose
3d4f1fa26f0e Uploaded devteam parents: diff changeset	101
3d4f1fa26f0e Uploaded devteam parents: diff changeset	102 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.
3d4f1fa26f0e Uploaded devteam parents: diff changeset	103
3d4f1fa26f0e Uploaded devteam parents: diff changeset	104 @dataset_collections@
3d4f1fa26f0e Uploaded devteam parents: diff changeset	105
3d4f1fa26f0e Uploaded devteam parents: diff changeset	106 @description@
3d4f1fa26f0e Uploaded devteam parents: diff changeset	107
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	108
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	109 DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN +
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	110 DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	111 includes enough anomalous values from chimeras and other artifacts to make the mean and
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	112 sd grossly misleading regarding the real distribution. Default value: 10.0.
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	113
3d4f1fa26f0e Uploaded devteam parents: diff changeset	114 HISTOGRAM_WIDTH=Integer
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	115 W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	116 Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	117 included. Default value: not set.
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	118
3d4f1fa26f0e Uploaded devteam parents: diff changeset	119 MINIMUM_PCT=Float
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	120 M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	121 have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05.
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	122
3d4f1fa26f0e Uploaded devteam parents: diff changeset	123 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	124 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	125 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	126
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	127 ASSUME_SORTED=Boolean
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	128 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	129 value: true. This option can be set to 'null' to clear the default value. Possible
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	130 values: {true, false}
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	131
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	132 @more_info@
3d4f1fa26f0e Uploaded devteam parents: diff changeset	133
3d4f1fa26f0e Uploaded devteam parents: diff changeset	134 </help>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	135 </tool>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	136
3d4f1fa26f0e Uploaded devteam parents: diff changeset	137

Mercurial > repos > devteam > picard

annotate picard_CollectInsertSizeMetrics.xml @ 16:6741a8ace658 draft