picard: picard_CollectInsertSizeMetrics.xml annotate

annotate picard_CollectInsertSizeMetrics.xml @ 20:2a17c789e0a5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a

author	iuc
date	Tue, 19 Jun 2018 11:28:49 -0400
parents	5053a18d9bc8
children	585027e65f3b

rev	line source
19 5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73 iuc parents: 14 diff changeset	1 <tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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>
20 2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a iuc parents: 19 diff changeset	5 <token name="@WRAPPER_VERSION@">1</token>
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	6 </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	7 <expand macro="requirements">
19 5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73 iuc parents: 14 diff changeset	8 <requirement type="package" version="3.4.1">r-base</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	9 </expand>
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	10 <command detect_errors="exit_code"><![CDATA[
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	11 @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	12 @symlink_element_identifier@
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	13 ##set up input files
3d4f1fa26f0e Uploaded devteam parents: diff changeset	14
3d4f1fa26f0e Uploaded devteam parents: diff changeset	15 #set $reference_fasta_filename = "localref.fa"
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	16
19 5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73 iuc parents: 14 diff changeset	17 @handle_reference_source@
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	18
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	19 picard
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	20 CollectInsertSizeMetrics
14 465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f devteam parents: 13 diff changeset	21 INPUT='$escaped_element_identifier'
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	22 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	23 HISTOGRAM_FILE="${histFile}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	24 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	25
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	26 #if str( $hist_width ):
3d4f1fa26f0e Uploaded devteam parents: diff changeset	27 HISTOGRAM_WIDTH="${hist_width}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	28 #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	29
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	30 MINIMUM_PCT="${min_pct}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	31 REFERENCE_SEQUENCE="${reference_fasta_filename}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	32 ASSUME_SORTED="${assume_sorted}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	33 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	34
3d4f1fa26f0e Uploaded devteam parents: diff changeset	35 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	36 QUIET=true
3d4f1fa26f0e Uploaded devteam parents: diff changeset	37 VERBOSITY=ERROR
20 2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a iuc parents: 19 diff changeset	38 @TMPDIR_OPTION@
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	39
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	40 ]]></command>
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	41 <inputs>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	42 <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	43 <conditional name="reference_source">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	44 <param name="reference_source_selector" type="select" label="Load reference genome from">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	45 <option value="cached">Local cache</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	46 <option value="history">History</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	47 </param>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	48 <when value="cached">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	49 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	50 <options from_data_table="all_fasta">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	51 </options>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	52 <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	53 </param>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	54 </when>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	55 <when value="history">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	56 <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	57 </when>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	58 </conditional>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	59 <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	60 <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	61 <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	62 <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	63 <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	64 <option value="ALL_READS" selected="True">All reads</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	65 <option value="SAMPLE">Sample</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	66 <option value="LIBRARY">Library</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	67 <option value="READ_GROUP">Read group</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	68 </param>
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	69
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	70 <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	71
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	72 </inputs>
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 <outputs>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	75 <data format="tabular" name="outFile"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	76 <data format="pdf" name="histFile"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	77 </outputs>
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	78
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	79 <tests>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	80 <test>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	81 <param name="metric_accumulation_level" value="ALL_READS"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	82 <param name="deviations" value="10.0" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	83 <param name="hist_width" value="500" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	84 <param name="min_pct" value="0.05" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	85 <param name="assume_sorted" value="true" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	86 <param name="reference_source_selector" value="history" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	87 <param name="ref_file" value="picard_CollectInsertSizeMetrics_ref.fa" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	88 <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	89 <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	90 </test>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	91 </tests>
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	92
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	93
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	94 <help>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	95
3d4f1fa26f0e Uploaded devteam parents: diff changeset	96 .. class:: infomark
3d4f1fa26f0e Uploaded devteam parents: diff changeset	97
3d4f1fa26f0e Uploaded devteam parents: diff changeset	98 Purpose
3d4f1fa26f0e Uploaded devteam parents: diff changeset	99
3d4f1fa26f0e Uploaded devteam parents: diff changeset	100 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	101
3d4f1fa26f0e Uploaded devteam parents: diff changeset	102 @dataset_collections@
3d4f1fa26f0e Uploaded devteam parents: diff changeset	103
3d4f1fa26f0e Uploaded devteam parents: diff changeset	104 @description@
3d4f1fa26f0e Uploaded devteam parents: diff changeset	105
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	106
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	107 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	108 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	109 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	110 sd grossly misleading regarding the real distribution. Default value: 10.0.
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	111
3d4f1fa26f0e Uploaded devteam parents: diff changeset	112 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	113 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	114 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	115 included. Default value: not set.
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	116
3d4f1fa26f0e Uploaded devteam parents: diff changeset	117 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	118 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	119 have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05.
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	120
3d4f1fa26f0e Uploaded devteam parents: diff changeset	121 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	122 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	123 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	124
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	125 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	126 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	127 value: true. This option can be set to 'null' to clear the default value. Possible
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	128 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	129
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	130 @more_info@
3d4f1fa26f0e Uploaded devteam parents: diff changeset	131
3d4f1fa26f0e Uploaded devteam parents: diff changeset	132 </help>
19 5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73 iuc parents: 14 diff changeset	133 <expand macro="citations" />
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	134 </tool>

Mercurial > repos > devteam > picard

annotate picard_CollectInsertSizeMetrics.xml @ 20:2a17c789e0a5 draft