Mercurial > repos > devteam > picard
comparison picard_CollectInsertSizeMetrics.xml @ 13:7e6fd3d0f16e draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author | devteam |
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date | Tue, 06 Dec 2016 10:04:41 -0500 |
parents | 05087b27692a |
children | 465cbb0cf2eb |
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12:05087b27692a | 13:7e6fd3d0f16e |
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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 <= Histogram_WIDTH will be | 116 Also, when calculating mean and standard deviation, only bins <= 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 |