deeptools: bamCompare.xml annotate

annotate bamCompare.xml @ 30:5231f398d784 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty

author	bgruening
date	Tue, 20 Oct 2015 14:43:12 -0400
parents	3a2aab18a217
children

rev	line source
28 f7712a057440 new bugfix release bgruening parents: 27 diff changeset	1 <tool id="deeptools_bamCompare" name="bamCompare" version="@WRAPPER_VERSION@.0">
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	2 <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	3 <macros>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	4 <token name="@BINARY@">bamCompare</token>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	5 <import>deepTools_macros.xml</import>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	6 </macros>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	7 <expand macro="requirements" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	8 <command>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	9 <![CDATA[
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	10 bamCompare
2ad3b027dfcd Uploaded bgruening parents: diff changeset	11
2ad3b027dfcd Uploaded bgruening parents: diff changeset	12 @THREADS@
2ad3b027dfcd Uploaded bgruening parents: diff changeset	13
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	14 --bamfile1 '$bamFile1'
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	15 -bai1 '${bamFile1.metadata.bam_index}'
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	16 --bamfile2 '$bamFile2'
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	17 -bai2 '${bamFile2.metadata.bam_index}'
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	18
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	19 --outFileName '$outFileName'
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	20 --outFileFormat '$outFileFormat'
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	21
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	22 --fragmentLength $fragmentLength
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	23 --binSize $binSize
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	24
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	25 #if $scaling.method == 'SES':
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	26 --scaleFactorsMethod SES
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	27 --sampleLength $scaling.sampleLength
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	28 #elif $scaling.method == 'readCount':
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	29 --scaleFactorsMethod readCount
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	30 #elif $scaling.method == 'own':
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	31 --scaleFactors '$scaling.scaleFactor1:$scaling.scaleFactor2'
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	32 #end if
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	33
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	34 --ratio $comparison.type
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	35
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	36 #if $comparison.type=='subtract':
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	37 #if $comparison.normalization.type=='rpkm':
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	38 --normalizeUsingRPKM
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	39 #elif $comparison.normalization.type=='1x':
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	40
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	41 #if $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	42 --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	43 #else:
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	44 --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	45 #end if
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	46
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	47 #end if
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	48 #elif $comparison.type in ['ratio','log2']:
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	49 --pseudocount $comparison.pseudocount
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	50 #end if
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	51
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	52 #if str($region).strip() != '':
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	53 --region '$region'
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	54 #end if
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	55
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	56 #if $advancedOpt.showAdvancedOpt == "yes":
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	57 #if $advancedOpt.smoothLength:
2ad3b027dfcd Uploaded bgruening parents: diff changeset	58 --smoothLength '$advancedOpt.smoothLength'
2ad3b027dfcd Uploaded bgruening parents: diff changeset	59 #end if
2ad3b027dfcd Uploaded bgruening parents: diff changeset	60
2ad3b027dfcd Uploaded bgruening parents: diff changeset	61 $advancedOpt.doNotExtendPairedEnds
2ad3b027dfcd Uploaded bgruening parents: diff changeset	62 $advancedOpt.ignoreDuplicates
2ad3b027dfcd Uploaded bgruening parents: diff changeset	63
2ad3b027dfcd Uploaded bgruening parents: diff changeset	64 #if $advancedOpt.minMappingQuality:
2ad3b027dfcd Uploaded bgruening parents: diff changeset	65 --minMappingQuality '$advancedOpt.minMappingQuality'
2ad3b027dfcd Uploaded bgruening parents: diff changeset	66 #end if
2ad3b027dfcd Uploaded bgruening parents: diff changeset	67
2ad3b027dfcd Uploaded bgruening parents: diff changeset	68 --missingDataAsZero $advancedOpt.missingDataAsZero
2ad3b027dfcd Uploaded bgruening parents: diff changeset	69
2ad3b027dfcd Uploaded bgruening parents: diff changeset	70 #if str($advancedOpt.ignoreForNormalization).strip() != '':
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	71 --ignoreForNormalization '$advancedOpt.ignoreForNormalization'
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	72 #end if
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	73 #if $samFlag:
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	74 --samFlag $samFlag
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	75 #end if
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	76 #end if
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	77 ]]>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	78 </command>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	79 <inputs>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	80 <param name="bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	81 help="The BAM file must be sorted."/>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	82 <param name="bamFile2" format="bam" type="data" label="Second BAM file (e.g. control sample)"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	83 help="The BAM file must be sorted."/>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	84 <param name="fragmentLength" type="integer" value="200" min="1"
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	85 label="Length of the average fragment size"
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	86 help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. Warning the fragment length affects the normalization to 1x (see "normalize coverage to 1x"). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). NOTE: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length. (--fragmentLength)"/>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	87
2ad3b027dfcd Uploaded bgruening parents: diff changeset	88 <param name="binSize" type="integer" value="50" min="1"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	89 label="Bin size in bp"
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	90 help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. (--binSize)"/>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	91
2ad3b027dfcd Uploaded bgruening parents: diff changeset	92 <conditional name="scaling">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	93 <param name="method" type="select"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	94 label="Method to use for scaling the largest sample to the smallest">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	95 <option value="readCount" selected="true">read count</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	96 <option value="SES">signal extraction scaling (SES), check the bamFingerprint plot before using it!</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	97 <option value="own">enter own scaling factors</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	98 </param>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	99 <when value="SES">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	100 <param name="sampleLength" type="integer" value="1000" min="10"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	101 label="Length in base pairs used to sample the genome and compute the size or scaling factors to compare the two BAM files "
2ad3b027dfcd Uploaded bgruening parents: diff changeset	102 help="The default is fine. Only change it if you know what you are doing" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	103 </when>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	104 <when value="readCount" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	105 <when value="own">
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	106 <expand macro="scaleFactor" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	107 </when>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	108 </conditional>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	109
2ad3b027dfcd Uploaded bgruening parents: diff changeset	110 <conditional name="comparison">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	111 <param name="type" type="select"
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	112 label="How to compare the two files"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	113 help="The default is to output the log2ratio between the two samples.
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	114 The reciprocal ratio returns the negative of the inverse of the ratio if
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	115 the ratio is less than 0. The resulting values are interpreted as negative fold changes.">
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	116 <option value="log2" selected="true">Compute log2 of the number of reads ratio</option>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	117 <option value="ratio">Compute the ratio of the number of reads</option>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	118 <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	119 <option value="add">Compute the sum of number of reads</option>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	120 <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	121 </param>
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	122 <when value="log2">
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	123 <expand macro="pseudocount" />
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	124 </when>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	125 <when value="ratio">
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	126 <expand macro="pseudocount" />
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	127 </when>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	128 <when value="add" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	129 <when value="reciprocal_ratio">
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	130 <expand macro="pseudocount" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	131 </when>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	132 <when value="subtract">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	133 <conditional name="normalization">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	134 <param name="type" type="select" label="Normalization method" >
2ad3b027dfcd Uploaded bgruening parents: diff changeset	135 <option value="1x">Normalize coverage to 1x</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	136 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	137 <option value="no">Do not normalize or scale</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	138 </param>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	139 <when value="rpkm" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	140 <when value="no" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	141 <when value="1x">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	142 <expand macro="effectiveGenomeSize" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	143 </when>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	144 </conditional>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	145 </when>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	146 </conditional>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	147
2ad3b027dfcd Uploaded bgruening parents: diff changeset	148 <param name="outFileFormat" type="select" label="Coverage file format">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	149 <option value="bigwig" selected="true">bigwig</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	150 <option value="bedgraph">bedgraph</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	151 </param>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	152 <expand macro="region_limit_operation" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	153 <conditional name="advancedOpt">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	154 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
2ad3b027dfcd Uploaded bgruening parents: diff changeset	155 <option value="no" selected="true">no</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	156 <option value="yes">yes</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	157 </param>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	158 <when value="no" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	159 <when value="yes">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	160 <param name="smoothLength" type="integer" value="1" optional="true" min="1"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	161 label="Smooth values using the following length (in bp)"
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	162 help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied. (--smoothLength)"/>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	163 <expand macro="doNotExtendPairedEnds" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	164 <expand macro="ignoreDuplicates" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	165 <expand macro="minMappingQuality" />
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	166 <expand macro="missingDataAsZero" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	167 <param name="ignoreForNormalization" type="text" value="" size="50"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	168 label="regions that should be excluded for calculating the scaling factor"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	169 help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	170 <expand macro="samFlag" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	171 </when>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	172 </conditional>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	173 </inputs>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	174 <outputs>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	175 <data format="bigwig" name="outFileName">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	176 <change_format>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	177 <when input="outFileFormat" value="bigwig" format="bigwig" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	178 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	179 </change_format>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	180 </data>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	181 </outputs>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	182 <tests>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	183 <test>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	184 <param name="bamFile1" value="bowtie2-test1.bam" ftype="bam" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	185 <param name="bamFile2" value="bowtie2-test1.bam" ftype="bam" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	186 <param name="showAdvancedOpt" value="no" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	187 <param name="outFileFormat" value="bigwig" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	188 <param name="fragmentLength" value="100" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	189 <param name="outFileFormat" value="bedgraph" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	190 <param name="binSize" value="5" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	191 <param name="type" value="ratio" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	192 <output name="outFileName" file="bamCompare_result1.bg" ftype="bedgraph" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	193 </test>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	194 </tests>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	195 <help>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	196 <![CDATA[
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	197 What it does
2ad3b027dfcd Uploaded bgruening parents: diff changeset	198
2ad3b027dfcd Uploaded bgruening parents: diff changeset	199 This tool compares two BAM files based on the number of mapped reads. To
28 f7712a057440 new bugfix release bgruening parents: 27 diff changeset	200 compare the BAM files, the genome is partitioned into bins of equal size, then
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	201 the number of reads found in each BAM file is counted for such bins and
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	202 finally a summarizing value is reported. This value can be the ratio of the
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	203 number of reads per bin, the log2 of the ratio or the difference. This tool
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	204 can normalize the number of reads on each BAM file using the SES method
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	205 proposed by Diaz et al. (2012). "Normalization, bias correction, and peak
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	206 calling for ChIP-seq". Statistical applications in genetics and molecular
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	207 biology, 11(3). Normalization based on read counts is also available. The
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	208 output is either a bedgraph or a bigwig file containing the bin location and
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	209 the resulting comparison values. By default, if reads are mated, the fragment
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	210 length reported in the BAM file is used. In the case of paired-end mapping
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	211 each read mate is treated independently to avoid a bias when a mixture of
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	212 concordant and discordant pairs is present. This means that each end will be
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	213 extended to match the fragment length.
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	214
2ad3b027dfcd Uploaded bgruening parents: diff changeset	215
2ad3b027dfcd Uploaded bgruening parents: diff changeset	216 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
2ad3b027dfcd Uploaded bgruening parents: diff changeset	217
2ad3b027dfcd Uploaded bgruening parents: diff changeset	218
2ad3b027dfcd Uploaded bgruening parents: diff changeset	219 You can find more details on the bamCompare wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
2ad3b027dfcd Uploaded bgruening parents: diff changeset	220
2ad3b027dfcd Uploaded bgruening parents: diff changeset	221
2ad3b027dfcd Uploaded bgruening parents: diff changeset	222 Output files:
2ad3b027dfcd Uploaded bgruening parents: diff changeset	223
2ad3b027dfcd Uploaded bgruening parents: diff changeset	224 - same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files.
2ad3b027dfcd Uploaded bgruening parents: diff changeset	225
2ad3b027dfcd Uploaded bgruening parents: diff changeset	226 -----
2ad3b027dfcd Uploaded bgruening parents: diff changeset	227
2ad3b027dfcd Uploaded bgruening parents: diff changeset	228 @REFERENCES@
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	229 ]]>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	230 </help>
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	231 <expand macro="citations" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	232 </tool>

Mercurial > repos > bgruening > deeptools

annotate bamCompare.xml @ 30:5231f398d784 draft