Mercurial > repos > devteam > picard
annotate picard_CollectAlignmentSummaryMetrics.xml @ 12:05087b27692a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author | devteam |
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date | Sun, 27 Nov 2016 15:11:50 -0500 |
parents | 777ccdd1d6e4 |
children | 7e6fd3d0f16e |
rev | line source |
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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.1"> |
5 | 2 <description>writes a file containing summary alignment metrics</description> |
3 <macros> | |
4 <import>picard_macros.xml</import> | |
5 </macros> | |
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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6 <expand macro="requirements" /> |
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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7 <command detect_errors="exit_code"><![CDATA[ |
5 | 8 @java_options@ |
9 ##set up input files | |
10 | |
11 #set $reference_fasta_filename = "localref.fa" | |
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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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12 |
5 | 13 #if str( $reference_source.reference_source_selector ) == "history": |
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
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14 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && |
5 | 15 #else: |
16 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | |
17 #end if | |
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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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18 |
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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diff
changeset
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19 picard |
5 | 20 CollectAlignmentSummaryMetrics |
21 INPUT="${inputFile}" | |
22 OUTPUT="${outFile}" | |
23 MAX_INSERT_SIZE=${maxinsert} | |
24 #for $sequence in $adapters: | |
25 ADAPTER_SEQUENCE="${sequence.adapter}" | |
26 #end for | |
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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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27 #for $level in str($metric_accumulation_level).split(','): |
777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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28 METRIC_ACCUMULATION_LEVEL="${level}" |
777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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29 #end for |
5 | 30 IS_BISULFITE_SEQUENCED="${bisulphite}" |
10
777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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31 |
5 | 32 REFERENCE_SEQUENCE="${reference_fasta_filename}" |
10
777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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33 |
5 | 34 ASSUME_SORTED="${assume_sorted}" |
35 | |
36 VALIDATION_STRINGENCY="${validation_stringency}" | |
37 QUIET=true | |
38 VERBOSITY=ERROR | |
39 | |
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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40 ]]></command> |
5 | 41 <inputs> |
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."/> | |
43 <conditional name="reference_source"> | |
44 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
45 <option value="cached">Local cache</option> | |
46 <option value="history">History</option> | |
47 </param> | |
48 <when value="cached"> | |
49 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> | |
50 <options from_data_table="all_fasta"> | |
51 </options> | |
52 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
53 </param> | |
54 </when> | |
55 <when value="history"> | |
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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56 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> |
5 | 57 </when> |
58 </conditional> | |
59 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL"> | |
60 <option value="ALL_READS" selected="True">All reads</option> | |
61 <option value="SAMPLE">Sample</option> | |
62 <option value="LIBRARY">Library</option> | |
63 <option value="READ_GROUP">Read group</option> | |
64 </param> | |
65 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> | |
66 <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/> | |
67 <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences"> | |
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5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
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68 <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/> |
5 | 69 </repeat> |
9
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
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70 <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/> |
5 | 71 <expand macro="VS" /> |
10
777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
9
diff
changeset
|
72 |
5 | 73 </inputs> |
74 <outputs> | |
75 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> | |
76 </outputs> | |
77 <tests> | |
78 <test> | |
79 <param name="bisulphite" value="false" /> | |
80 <param name="sorted" value="true" /> | |
81 <param name="adaptors" value="" /> | |
82 <param name="maxinsert" value="100000" /> | |
83 <param name="reference_source_selector" value="history" /> | |
84 <param name="ref_file" value="picard_CASM_ref.fa" /> | |
85 <param name="inputFile" value="picard_CASM.bam" ftype="bam" /> | |
86 <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/> | |
87 </test> | |
88 </tests> | |
89 <help> | |
90 | |
91 .. class:: infomark | |
92 | |
93 **Purpose** | |
94 | |
95 Reads a SAM or BAM file and writes a file containing summary alignment metrics. | |
96 | |
97 @dataset_collections@ | |
98 | |
99 @description@ | |
100 | |
101 MAX_INSERT_SIZE=Integer Paired end reads above this insert size will be considered chimeric along with | |
102 inter-chromosomal pairs. Default value: 100000. | |
103 | |
104 ADAPTER_SEQUENCE=String List of adapter sequences to use when processing the alignment metrics This option may | |
105 be specified 0 or more times. | |
106 | |
107 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel | |
108 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, | |
109 LIBRARY, READ_GROUP} This option may be specified 0 or more times. | |
110 | |
111 IS_BISULFITE_SEQUENCED=Boolean | |
112 BS=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. | |
113 | |
114 | |
115 REFERENCE_SEQUENCE=File | |
116 R=File Reference sequence fasta Default value: null. | |
117 | |
118 ASSUME_SORTED=Boolean | |
119 AS=Boolean If true (default), then the sort order in the header file will be ignored. | |
120 | |
121 @more_info@ | |
122 | |
123 </help> | |
124 </tool> | |
125 | |
126 |