Mercurial > repos > devteam > picard_122_up
comparison picard_MeanQualityByCycle.xml @ 0:b76a4f17bbbb draft
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author | devteam |
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date | Thu, 23 Oct 2014 11:31:30 -0400 |
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-1:000000000000 | 0:b76a4f17bbbb |
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1 <tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="1.122.0"> | |
2 <description>chart distribution of base qualities</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( $reference_source.ref_file.fields.path ) | |
21 #end if | |
22 | |
23 java -jar \$JAVA_JAR_PATH/MeanQualityByCycle.jar | |
24 INPUT="${inputFile}" | |
25 OUTPUT="${outFile}" | |
26 CHART_OUTPUT="${pdfFile}" | |
27 REFERENCE_SEQUENCE="${reference_fasta_filename}" | |
28 ALIGNED_READS_ONLY="${aligned_reads_only}" | |
29 PF_READS_ONLY="${pf_reads_only}" | |
30 | |
31 ASSUME_SORTED="${assume_sorted}" | |
32 | |
33 VALIDATION_STRINGENCY="${validation_stringency}" | |
34 QUIET=true | |
35 VERBOSITY=ERROR | |
36 | |
37 </command> | |
38 <inputs> | |
39 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> | |
40 <conditional name="reference_source"> | |
41 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
42 <option value="cached">Local cache</option> | |
43 <option value="history">History</option> | |
44 </param> | |
45 <when value="cached"> | |
46 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> | |
47 <options from_data_table="all_fasta"> | |
48 </options> | |
49 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
50 </param> | |
51 </when> | |
52 <when value="history"> | |
53 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> | |
54 </when> | |
55 </conditional> | |
56 <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/> | |
57 <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/> | |
58 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> | |
59 | |
60 <expand macro="VS" /> | |
61 | |
62 </inputs> | |
63 | |
64 <outputs> | |
65 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> | |
66 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> | |
67 </outputs> | |
68 | |
69 <tests> | |
70 <test> | |
71 <param name="assume_sorted" value="true" /> | |
72 <param name="aligned_reads_only" value="false" /> | |
73 <param name="pf_reads_only" value="false" /> | |
74 <param name="reference_source_selector" value="history" /> | |
75 <param name="ref_file" value="picard_MeanQualityByCycle_ref.fa" /> | |
76 <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam" /> | |
77 <output name="outFile" file="picard_MeanQualityByCycle_test1.tab" ftype="tabular" lines_diff="4"/> | |
78 </test> | |
79 </tests> | |
80 | |
81 <stdio> | |
82 <exit_code range="1:" level="fatal"/> | |
83 </stdio> | |
84 | |
85 <help> | |
86 | |
87 .. class:: infomark | |
88 | |
89 **Purpose** | |
90 | |
91 Program to chart the distribution of base qualities by cycle within reads supplied in a SAM or BAM dataset. | |
92 | |
93 @dataset_collections@ | |
94 | |
95 @description@ | |
96 | |
97 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: | |
98 false. Possible values: {true, false} | |
99 | |
100 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. | |
101 This option can be set to 'null' to clear the default value. Possible values: {true, | |
102 false} | |
103 | |
104 ASSUME_SORTED=Boolean | |
105 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True | |
106 | |
107 @more_info@ | |
108 | |
109 </help> | |
110 </tool> | |
111 | |
112 |