Mercurial > repos > devteam > picard_plus
comparison picard_CollectAlignmentSummaryMetrics.xml @ 0:4419e9980172 draft
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author | devteam |
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date | Thu, 23 Oct 2014 12:03:34 -0400 |
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-1:000000000000 | 0:4419e9980172 |
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1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="1.122.0"> | |
2 <description>writes a file containing summary alignment metrics</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.122.0">picard</requirement> | |
5 </requirements> | |
6 | |
7 <macros> | |
8 <import>picard_macros.xml</import> | |
9 </macros> | |
10 | |
11 <command> | |
12 @java_options@ | |
13 ##set up input files | |
14 | |
15 #set $reference_fasta_filename = "localref.fa" | |
16 | |
17 #if str( $reference_source.reference_source_selector ) == "history": | |
18 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && | |
19 #else: | |
20 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | |
21 #end if | |
22 | |
23 java -jar \$JAVA_JAR_PATH/CollectAlignmentSummaryMetrics.jar | |
24 INPUT="${inputFile}" | |
25 OUTPUT="${outFile}" | |
26 MAX_INSERT_SIZE=${maxinsert} | |
27 #for $sequence in $adapters: | |
28 ADAPTER_SEQUENCE="${sequence.adapter}" | |
29 #end for | |
30 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" | |
31 IS_BISULFITE_SEQUENCED="${bisulphite}" | |
32 | |
33 REFERENCE_SEQUENCE="${reference_fasta_filename}" | |
34 | |
35 ASSUME_SORTED="${assume_sorted}" | |
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="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL"> | |
61 <option value="ALL_READS" selected="True">All reads</option> | |
62 <option value="SAMPLE">Sample</option> | |
63 <option value="LIBRARY">Library</option> | |
64 <option value="READ_GROUP">Read group</option> | |
65 </param> | |
66 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> | |
67 <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/> | |
68 <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences"> | |
69 <param name="adapter" type="text" size="50" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/> | |
70 </repeat> | |
71 <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" size="20" help="MAX_INSERT_SIZE"/> | |
72 | |
73 <expand macro="VS" /> | |
74 | |
75 </inputs> | |
76 | |
77 <outputs> | |
78 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> | |
79 </outputs> | |
80 | |
81 <stdio> | |
82 <exit_code range="1:" level="fatal"/> | |
83 </stdio> | |
84 | |
85 | |
86 <tests> | |
87 <test> | |
88 <param name="bisulphite" value="false" /> | |
89 <param name="sorted" value="true" /> | |
90 <param name="adaptors" value="" /> | |
91 <param name="maxinsert" value="100000" /> | |
92 <param name="reference_source_selector" value="history" /> | |
93 <param name="ref_file" value="picard_CASM_ref.fa" /> | |
94 <param name="inputFile" value="picard_CASM.bam" ftype="bam" /> | |
95 <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/> | |
96 </test> | |
97 </tests> | |
98 | |
99 <help> | |
100 | |
101 .. class:: infomark | |
102 | |
103 **Purpose** | |
104 | |
105 Reads a SAM or BAM file and writes a file containing summary alignment metrics. | |
106 | |
107 @dataset_collections@ | |
108 | |
109 @description@ | |
110 | |
111 MAX_INSERT_SIZE=Integer Paired end reads above this insert size will be considered chimeric along with | |
112 inter-chromosomal pairs. Default value: 100000. | |
113 | |
114 ADAPTER_SEQUENCE=String List of adapter sequences to use when processing the alignment metrics This option may | |
115 be specified 0 or more times. | |
116 | |
117 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel | |
118 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, | |
119 LIBRARY, READ_GROUP} This option may be specified 0 or more times. | |
120 | |
121 IS_BISULFITE_SEQUENCED=Boolean | |
122 BS=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. | |
123 | |
124 | |
125 REFERENCE_SEQUENCE=File | |
126 R=File Reference sequence fasta Default value: null. | |
127 | |
128 ASSUME_SORTED=Boolean | |
129 AS=Boolean If true (default), then the sort order in the header file will be ignored. | |
130 | |
131 @more_info@ | |
132 | |
133 </help> | |
134 </tool> | |
135 | |
136 |