comparison picard_MeanQualityByCylce.xml @ 118:21bf2afb895c draft

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author devteam
date Tue, 25 Feb 2014 18:55:09 -0500
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117:5fe20cda6a51 118:21bf2afb895c
1 <tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="1.106.0">
2 <description>Calculates mean quality</description>
3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
4 <command interpreter="bash">
5 <!-- generic_outformat_wrapper.sh MeanQualityByCycle $outFile $outputFormat
6 CHART_OUTPUT=File A file (with .pdf extension) to write the chart to. Required.
7
8 #if str( $ALIGNED_READS_ONLY ):
9 ALIGNED_READS_ONLY="${ALIGNED_READS_ONLY}"
10 #end if
11 #if str( $PF_READS_ONLY ):
12 PF_READS_ONLY="${PF_READS_ONLY}"
13 #end if
14 #if str( $INPUT ):
15 INPUT="${INPUT}"
16 #end if
17 #if str( $OUTPUT ):
18 OUTPUT="${OUTPUT}"
19 #end if
20 #if str( $REFERENCE_SEQUENCE ):
21 REFERENCE_SEQUENCE="${REFERENCE_SEQUENCE}"
22 #end if
23 #if str( $ASSUME_SORTED ):
24 ASSUME_SORTED="${ASSUME_SORTED}"
25 #end if
26 #if str( $STOP_AFTER ):
27 STOP_AFTER="${STOP_AFTER}"
28 #end if
29
30 VALIDATION_STRINGENCY=LENIENT
31 QUIET=True
32 TMP_DIR="${__new_file_path__}" -->
33 </command>
34
35 <stdio>
36 <exit_code range="0" level="warning" description="Tool finished correctly" />
37 </stdio>
38
39 <inputs>
40 <!--
41 <param format="XXCHANGEMEEE" name="ALIGNED_READS_ONLY" type="boolean" label="If set to true, calculate mean quality over aligned reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
42 <param format="XXCHANGEMEEE" name="PF_READS_ONLY" type="boolean" label="If set to true calculate mean quality over PF reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
43 <param format="XXCHANGEMEEE" name="INPUT" type="data" label="Input SAM or BAM file. Required." help="" />
44 <param format="XXCHANGEMEEE" name="OUTPUT" type="data" label="File to write the output to. Required." help="" />
45 <param format="XXCHANGEMEEE" name="REFERENCE_SEQUENCE" type="data" label="Reference sequence fasta Default value: null." help="" />
46 <param format="XXCHANGEMEEE" name="ASSUME_SORTED" type="boolean" label="If true (default), then the sort order in the header file will be ignored. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
47 <param format="XXCHANGEMEEE" name="STOP_AFTER" type="string" label="Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value." help="" />
48 -->
49 </inputs>
50 <outputs>
51 <!--
52 <data name="outFile" format="XXCHANGEMEEE">
53
54 </data>
55 -->
56 </outputs>
57 <tests>
58 <test>
59 <!-- Here is a command line that works:
60 java -jar ...
61 -->
62 <!--
63 <param name="inputFile" value="XXCHANGEMEE-input" />
64 <output name="outFile" file="XXCHANGEMEE-correct-output" lines_diff="2" ftype="XXCHANGEMEE" />
65 -->
66 </test>
67 </tests>
68 <help>
69 Picard documentation says:
70
71
72 MeanQualityByCycle
73
74 Usage: program [options...]
75
76 Option Description
77 CHART_OUTPUT=File A file (with .pdf extension) to write the chart to. Required.
78 ALIGNED_READS_ONLY=Boolean If set to true, calculate mean quality over aligned reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
79 PF_READS_ONLY=Boolean If set to true calculate mean quality over PF reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
80 INPUT=File Input SAM or BAM file. Required.
81 OUTPUT=File File to write the output to. Required.
82 REFERENCE_SEQUENCE=File Reference sequence fasta Default value: null.
83 ASSUME_SORTED=Boolean If true (default), then the sort order in the header file will be ignored. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
84 STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value.
85
86
87 </help>
88 </tool>