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comparison picard_EstimateLibraryComplexity.xml @ 7:08f69add4d06 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:36 -0500
parents 2589e6207cb4
children e417b1d6288d
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6:961236c5ec73 7:08f69add4d06
2 <description>assess sequence library complexity from read sequences</description> 2 <description>assess sequence library complexity from read sequences</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command> 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 9
10 java -jar \$JAVA_JAR_PATH/picard.jar 10 picard
11 EstimateLibraryComplexity 11 EstimateLibraryComplexity
12 12
13 INPUT="${inputFile}" 13 INPUT="${inputFile}"
14 OUTPUT="${outFile}" 14 OUTPUT="${outFile}"
15 15
23 23
24 VALIDATION_STRINGENCY="${validation_stringency}" 24 VALIDATION_STRINGENCY="${validation_stringency}"
25 QUIET=true 25 QUIET=true
26 VERBOSITY=ERROR 26 VERBOSITY=ERROR
27 27
28 </command> 28 ]]></command>
29 <inputs> 29 <inputs>
30 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> 30 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
31 <param name="min_identical_bases" type="integer" value="5" label="The minimum number of bases at the starts of reads that must be identical for reads to be grouped together for duplicate detection" help="MIN_IDENTICAL_BASES; In effect total_reads / 4^max_id_bases reads will be compared at a time, so lower numbers will produce more accurate results but consume exponentially more memory and CPU; default=5"/> 31 <param name="min_identical_bases" type="integer" value="5" label="The minimum number of bases at the starts of reads that must be identical for reads to be grouped together for duplicate detection" help="MIN_IDENTICAL_BASES; In effect total_reads / 4^max_id_bases reads will be compared at a time, so lower numbers will produce more accurate results but consume exponentially more memory and CPU; default=5"/>
32 <param name="max_diff_rate" type="float" value="0.03" label="The maximum rate of differences between two reads to call them identical" help="MAX_DIFF_RATE; default=0.03"/> 32 <param name="max_diff_rate" type="float" value="0.03" label="The maximum rate of differences between two reads to call them identical" help="MAX_DIFF_RATE; default=0.03"/>
33 <param name="min_mean_quality" type="integer" min="0" max="93" value="20" label="The minimum mean quality of the bases in a read pair for the read to be analyzed" help="MIN_MEAN_QUALITY; Reads with lower average quality are filtered out and not considered in any calculations; default=20"/> 33 <param name="min_mean_quality" type="integer" min="0" max="93" value="20" label="The minimum mean quality of the bases in a read pair for the read to be analyzed" help="MIN_MEAN_QUALITY; Reads with lower average quality are filtered out and not considered in any calculations; default=20"/>
61 <param name="validation_stringency" value="LENIENT"/> 61 <param name="validation_stringency" value="LENIENT"/>
62 <output name="outFile" file="picard_EstimateLibraryComplexity_test1.tab" ftype="tabular" lines_diff="4"/> 62 <output name="outFile" file="picard_EstimateLibraryComplexity_test1.tab" ftype="tabular" lines_diff="4"/>
63 </test> 63 </test>
64 </tests> 64 </tests>
65 65
66 <stdio>
67 <exit_code range="1:" level="fatal"/>
68 </stdio>
69 66
70 <help> 67 <help>
71 68
72 **Purpose** 69 **Purpose**
73 70