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comparison picard_CollectInsertSizeMetrics.xml @ 13:7e6fd3d0f16e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:41 -0500
parents 05087b27692a
children 465cbb0cf2eb
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12:05087b27692a 13:7e6fd3d0f16e
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="3.3.1">r</requirement> 7 <requirement type="package" version="3.3.1">r</requirement>
8 </expand> 8 </expand>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 @java_options@ 10 @java_options@
11 @symlink_element_identifier@
11 ##set up input files 12 ##set up input files
12 13
13 #set $reference_fasta_filename = "localref.fa" 14 #set $reference_fasta_filename = "localref.fa"
14 15
15 #if str( $reference_source.reference_source_selector ) == "history": 16 #if str( $reference_source.reference_source_selector ) == "history":
16 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && 17 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
17 #else: 18 #else:
18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
19 #end if 20 #end if
20 21
21 picard 22 picard
22 CollectInsertSizeMetrics 23 CollectInsertSizeMetrics
23 INPUT="${inputFile}" 24 INPUT='$inputFile.element_identifier'
24 OUTPUT="${outFile}" 25 OUTPUT="${outFile}"
25 HISTOGRAM_FILE="${histFile}" 26 HISTOGRAM_FILE="${histFile}"
26 DEVIATIONS="${deviations}" 27 DEVIATIONS="${deviations}"
27 28
28 #if str( $hist_width ): 29 #if str( $hist_width ):
29 HISTOGRAM_WIDTH="${hist_width}" 30 HISTOGRAM_WIDTH="${hist_width}"
30 #end if 31 #end if
31 32
32 MINIMUM_PCT="${min_pct}" 33 MINIMUM_PCT="${min_pct}"
33 REFERENCE_SEQUENCE="${reference_fasta_filename}" 34 REFERENCE_SEQUENCE="${reference_fasta_filename}"
34 ASSUME_SORTED="${assume_sorted}" 35 ASSUME_SORTED="${assume_sorted}"
35 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" 36 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
36 37
37 VALIDATION_STRINGENCY="${validation_stringency}" 38 VALIDATION_STRINGENCY="${validation_stringency}"
38 QUIET=true 39 QUIET=true
39 VERBOSITY=ERROR 40 VERBOSITY=ERROR
40 41
41 ]]></command> 42 ]]></command>
42 <inputs> 43 <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 <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 <conditional name="reference_source">
45 <param name="reference_source_selector" type="select" label="Load reference genome from"> 46 <param name="reference_source_selector" type="select" label="Load reference genome from">
65 <option value="ALL_READS" selected="True">All reads</option> 66 <option value="ALL_READS" selected="True">All reads</option>
66 <option value="SAMPLE">Sample</option> 67 <option value="SAMPLE">Sample</option>
67 <option value="LIBRARY">Library</option> 68 <option value="LIBRARY">Library</option>
68 <option value="READ_GROUP">Read group</option> 69 <option value="READ_GROUP">Read group</option>
69 </param> 70 </param>
70 71
71 <expand macro="VS" /> 72 <expand macro="VS" />
72 73
73 </inputs> 74 </inputs>
74 75
75 <outputs> 76 <outputs>
76 <data format="tabular" name="outFile"/> 77 <data format="tabular" name="outFile"/>
77 <data format="pdf" name="histFile"/> 78 <data format="pdf" name="histFile"/>
78 </outputs> 79 </outputs>
79 80
80 <tests> 81 <tests>
81 <test> 82 <test>
82 <param name="metric_accumulation_level" value="ALL_READS"/> 83 <param name="metric_accumulation_level" value="ALL_READS"/>
83 <param name="deviations" value="10.0" /> 84 <param name="deviations" value="10.0" />
84 <param name="hist_width" value="500" /> 85 <param name="hist_width" value="500" />
88 <param name="ref_file" value="picard_CollectInsertSizeMetrics_ref.fa" /> 89 <param name="ref_file" value="picard_CollectInsertSizeMetrics_ref.fa" />
89 <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam" /> 90 <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam" />
90 <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/> 91 <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
91 </test> 92 </test>
92 </tests> 93 </tests>
93 94
94 95
95 <help> 96 <help>
96 97
97 .. class:: infomark 98 .. class:: infomark
98 99
99 **Purpose** 100 **Purpose**
102 103
103 @dataset_collections@ 104 @dataset_collections@
104 105
105 @description@ 106 @description@
106 107
107 108
108 DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN + 109 DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN +
109 DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically 110 DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically
110 includes enough anomalous values from chimeras and other artifacts to make the mean and 111 includes enough anomalous values from chimeras and other artifacts to make the mean and
111 sd grossly misleading regarding the real distribution. Default value: 10.0. 112 sd grossly misleading regarding the real distribution. Default value: 10.0.
112 113
113 HISTOGRAM_WIDTH=Integer 114 HISTOGRAM_WIDTH=Integer
114 W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. 115 W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail.
115 Also, when calculating mean and standard deviation, only bins &lt;= Histogram_WIDTH will be 116 Also, when calculating mean and standard deviation, only bins &lt;= Histogram_WIDTH will be
116 included. Default value: not set. 117 included. Default value: not set.
117 118
118 MINIMUM_PCT=Float 119 MINIMUM_PCT=Float
119 M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that 120 M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that
120 have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. 121 have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05.
121 122
122 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel 123 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
123 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, 124 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
124 LIBRARY, READ_GROUP} This option may be specified 0 or more times. 125 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
125 126
126 ASSUME_SORTED=Boolean 127 ASSUME_SORTED=Boolean
127 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default 128 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default
128 value: true. This option can be set to 'null' to clear the default value. Possible 129 value: true. This option can be set to 'null' to clear the default value. Possible
129 values: {true, false} 130 values: {true, false}
130 131
131 @more_info@ 132 @more_info@
132 133
133 </help> 134 </help>
134 </tool> 135 </tool>
135 136