deeptools: bamCorrelate.xml annotate

annotate bamCorrelate.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_bamCorrelate" name="bamCorrelate" version="@WRAPPER_VERSION@.0">
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	2 <description>correlates pairs of BAM files</description>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	3 <macros>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	4 <token name="@BINARY@">bamCorrelate</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 #set files=[]
2ad3b027dfcd Uploaded bgruening parents: diff changeset	11 #set labels=[]
2ad3b027dfcd Uploaded bgruening parents: diff changeset	12
2ad3b027dfcd Uploaded bgruening parents: diff changeset	13 @multiple_input_bams@
2ad3b027dfcd Uploaded bgruening parents: diff changeset	14
2ad3b027dfcd Uploaded bgruening parents: diff changeset	15 bamCorrelate
2ad3b027dfcd Uploaded bgruening parents: diff changeset	16
2ad3b027dfcd Uploaded bgruening parents: diff changeset	17 $mode.modeOpt
2ad3b027dfcd Uploaded bgruening parents: diff changeset	18
2ad3b027dfcd Uploaded bgruening parents: diff changeset	19 @THREADS@
2ad3b027dfcd Uploaded bgruening parents: diff changeset	20
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	21 --bamfiles '#echo "' '".join($files)#'
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	22 --labels '#echo "' '".join($labels)#'
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	23 --fragmentLength $fragmentLength
2ad3b027dfcd Uploaded bgruening parents: diff changeset	24 --corMethod $corMethod
2ad3b027dfcd Uploaded bgruening parents: diff changeset	25
2ad3b027dfcd Uploaded bgruening parents: diff changeset	26 --plotFile $outFileName
2ad3b027dfcd Uploaded bgruening parents: diff changeset	27
2ad3b027dfcd Uploaded bgruening parents: diff changeset	28 #if $output.showOutputSettings == "yes"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	29 --outRawCounts '$outFileRawCounts'
2ad3b027dfcd Uploaded bgruening parents: diff changeset	30 --outFileCorMatrix '$outFileCorMatrix'
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	31 --plotFileFormat '$output.outFileFormat'
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	32 #else:
2ad3b027dfcd Uploaded bgruening parents: diff changeset	33 --plotFileFormat 'png'
2ad3b027dfcd Uploaded bgruening parents: diff changeset	34 #end if
2ad3b027dfcd Uploaded bgruening parents: diff changeset	35
2ad3b027dfcd Uploaded bgruening parents: diff changeset	36 #if $mode.modeOpt == "bins":
2ad3b027dfcd Uploaded bgruening parents: diff changeset	37 --binSize '$mode.binSize'
28 f7712a057440 new bugfix release bgruening parents: 27 diff changeset	38 --distanceBetweenBins '$mode.distanceBetweenBins'
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	39 $mode.doNotRemoveOutliers
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	40 #else:
2ad3b027dfcd Uploaded bgruening parents: diff changeset	41 --BED $mode.region_file
2ad3b027dfcd Uploaded bgruening parents: diff changeset	42 #end if
2ad3b027dfcd Uploaded bgruening parents: diff changeset	43
2ad3b027dfcd Uploaded bgruening parents: diff changeset	44 #### options available in both modes
2ad3b027dfcd Uploaded bgruening parents: diff changeset	45 #if str($mode.region.value) != '':
2ad3b027dfcd Uploaded bgruening parents: diff changeset	46 --region '$mode.region'
2ad3b027dfcd Uploaded bgruening parents: diff changeset	47 #end if
2ad3b027dfcd Uploaded bgruening parents: diff changeset	48
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	49 #if $plotTitle and str($plotTitle).strip() != "":
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	50 --plotTitle '$plotTitle'
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	51 #end if
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	52 $plotNumbers
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	53 #if $mode.advancedOpt.showAdvancedOpt == "yes":
2ad3b027dfcd Uploaded bgruening parents: diff changeset	54
2ad3b027dfcd Uploaded bgruening parents: diff changeset	55 $mode.advancedOpt.doNotExtendPairedEnds
2ad3b027dfcd Uploaded bgruening parents: diff changeset	56 $mode.advancedOpt.ignoreDuplicates
2ad3b027dfcd Uploaded bgruening parents: diff changeset	57 $mode.advancedOpt.includeZeros
2ad3b027dfcd Uploaded bgruening parents: diff changeset	58
2ad3b027dfcd Uploaded bgruening parents: diff changeset	59 #if $mode.advancedOpt.minMappingQuality:
2ad3b027dfcd Uploaded bgruening parents: diff changeset	60 --minMappingQuality '$mode.advancedOpt.minMappingQuality'
2ad3b027dfcd Uploaded bgruening parents: diff changeset	61 #end if
2ad3b027dfcd Uploaded bgruening parents: diff changeset	62
2ad3b027dfcd Uploaded bgruening parents: diff changeset	63 #if $mode.advancedOpt.zMin:
2ad3b027dfcd Uploaded bgruening parents: diff changeset	64 --zMin $mode.advancedOpt.zMin
2ad3b027dfcd Uploaded bgruening parents: diff changeset	65 #end if
2ad3b027dfcd Uploaded bgruening parents: diff changeset	66 #if $mode.advancedOpt.zMax:
2ad3b027dfcd Uploaded bgruening parents: diff changeset	67 --zMax $mode.advancedOpt.zMax
2ad3b027dfcd Uploaded bgruening parents: diff changeset	68 #end if
2ad3b027dfcd Uploaded bgruening parents: diff changeset	69 --colorMap '$mode.advancedOpt.colorMap'
2ad3b027dfcd Uploaded bgruening parents: diff changeset	70
2ad3b027dfcd Uploaded bgruening parents: diff changeset	71 #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	72 ]]>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	73 </command>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	74
2ad3b027dfcd Uploaded bgruening parents: diff changeset	75 <inputs>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	76 <expand macro="multiple_input_bams" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	77
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	78 <param name="fragmentLength" type="integer" value="200" min="1"
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	79 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	80 help ="Reads will be extended to match this length unless they are paired-end,
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	81 in which case they will be extended to match the fragment length.
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	82 NOTE: If the BAM files contain mated and unmated paired-end reads, unmated reads will
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	83 be extended to match the fragment length. (--fragmentLength)"/>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	84
2ad3b027dfcd Uploaded bgruening parents: diff changeset	85 <param name="corMethod" type="select" label="Correlation method">
28 f7712a057440 new bugfix release bgruening parents: 27 diff changeset	86 <option value="spearman" selected="True">Spearman</option>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	87 <option value="pearson">Pearson</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	88 </param>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	89
2ad3b027dfcd Uploaded bgruening parents: diff changeset	90 <conditional name="mode">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	91 <param name="modeOpt" type="select" label="Choose computation mode"
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	92 help="In the bins mode, the correlation is computed based on equal
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	93 length bins. In the BED file mode, as list of genomic regions in BED
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	94 format has to be given. For each region in the BED file the number of
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	95 overlapping reads is counted in each of the BAM files.
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	96 Then the correlation is computed.">
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	97 <option value="bins" selected="true">Bins</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	98 <option value="BED-file">Limit correlation to certain regions (BED file)</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	99 </param>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	100 <when value="bins">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	101 <param name="binSize" type="integer" value="10000" min="1"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	102 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	103 help="Length in base pairs for a window used to sample the genome. (--binSize)"/>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	104
28 f7712a057440 new bugfix release bgruening parents: 27 diff changeset	105 <param name="distanceBetweenBins" type="integer" value="0" min="0"
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	106 label="Distance between bins"
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	107 help="By default, bamCorrelate considers consecutive bins of
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	108 the specified 'Bin size'. However, to reduce the
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	109 computation time, a larger distance between bins can
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	110 by given. Larger distances result in less bins being
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	111 considered. (--distanceBetweenBins)"/>
28 f7712a057440 new bugfix release bgruening parents: 27 diff changeset	112
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	113 <param name="doNotRemoveOutliers" type="boolean"
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	114 truevalue="--doNotRemoveOutliers" falsevalue="" label="Do not filter outliers"
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	115 help="By default, bins with very large counts are removed.
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	116 By setting this option, outliers will not be
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	117 removed. Bins with unusually large counts normally
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	118 correspond to regions in the genome that accumulate
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	119 lot of reads like satellite regions. If outliers are not
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	120 removed the pearson correlation will wrongly report a
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	121 very high correlation; that's why, by default,
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	122 bamCorrelate tries to remove outliers using
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	123 the median absolute deviation (MAD) method applying a
f7712a057440 new bugfix release bgruening parents: 27 diff changeset	124 threshold of 200 to only consider extremely large
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	125 deviations from the median. (--doNotRemoveOutliers)"/>
28 f7712a057440 new bugfix release bgruening parents: 27 diff changeset	126
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	127 <expand macro="bamCorrelate_mode_actions" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	128 </when>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	129 <when value="BED-file">
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	130 <param name="region_file" type="data" format="bed"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	131 label="Region file in BED format"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	132 help="Correlation is computed for the number of reads that overlap such regions."/>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	133 <expand macro="bamCorrelate_mode_actions" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	134 </when>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	135 </conditional>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	136 <expand macro="plotTitle" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	137 <expand macro="plotNumbers" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	138 <conditional name="output">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	139 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
2ad3b027dfcd Uploaded bgruening parents: diff changeset	140 <option value="no" selected="true">no</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	141 <option value="yes">yes</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	142 </param>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	143 <when value="no" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	144 <when value="yes">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	145 <expand macro="input_image_file_format"/>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	146 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	147 <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	148 </when>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	149 </conditional>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	150
2ad3b027dfcd Uploaded bgruening parents: diff changeset	151 </inputs>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	152 <outputs>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	153 <expand macro="output_image_file_format" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	154 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	155 <filter>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	156 ((
2ad3b027dfcd Uploaded bgruening parents: diff changeset	157 output['showOutputSettings'] == 'yes' and
2ad3b027dfcd Uploaded bgruening parents: diff changeset	158 output['saveRawCounts'] is True
2ad3b027dfcd Uploaded bgruening parents: diff changeset	159 ))
2ad3b027dfcd Uploaded bgruening parents: diff changeset	160 </filter>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	161 </data>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	162 <data format="tabular" name="outFileCorMatrix" label="${tool.name} on ${on_string}: correlation matrix">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	163 <filter>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	164 ((
2ad3b027dfcd Uploaded bgruening parents: diff changeset	165 output['showOutputSettings'] == 'yes' and
2ad3b027dfcd Uploaded bgruening parents: diff changeset	166 output['saveCorMatrix'] is True
2ad3b027dfcd Uploaded bgruening parents: diff changeset	167 ))
2ad3b027dfcd Uploaded bgruening parents: diff changeset	168 </filter>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	169 </data>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	170 </outputs>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	171 <tests>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	172 <test>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	173 <repeat name="input_files">
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	174 <param name="bamfile" 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	175 <param name="label" value="first BAM file" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	176 </repeat>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	177 <repeat name="input_files">
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	178 <param name="bamfile" 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	179 <param name="label" value="second BAM file" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	180 </repeat>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	181 <param name="modeOpt" value="bins" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	182 <param name="binSize" value="10" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	183 <param name="showOutputSettings" value="no" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	184 <output name="outFileName" file="bamCorrelate_result1.png" ftype="png" compare="sim_size" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	185 </test>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	186 </tests>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	187 <help>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	188 <![CDATA[
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	189 What it does
2ad3b027dfcd Uploaded bgruening parents: diff changeset	190
2ad3b027dfcd Uploaded bgruening parents: diff changeset	191 This tool is useful to assess the overall similarity of different BAM files. A typical application
2ad3b027dfcd Uploaded bgruening parents: diff changeset	192 is to check the correlation between replicates or published data sets.
2ad3b027dfcd Uploaded bgruening parents: diff changeset	193
2ad3b027dfcd Uploaded bgruening parents: diff changeset	194 The tool splits the genomes into bins of given length. For each bin, the number of reads
2ad3b027dfcd Uploaded bgruening parents: diff changeset	195 found in each BAM file is counted and a correlation (either Pearson or Spearman) is computed for all
2ad3b027dfcd Uploaded bgruening parents: diff changeset	196 pairs of BAM files. Finally, a heatmap is drawn based on the similarity of the samples.
2ad3b027dfcd Uploaded bgruening parents: diff changeset	197
2ad3b027dfcd Uploaded bgruening parents: diff changeset	198
2ad3b027dfcd Uploaded bgruening parents: diff changeset	199 .. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png
2ad3b027dfcd Uploaded bgruening parents: diff changeset	200 :alt: Heatmap of RNA Polymerase II ChIP-seq
2ad3b027dfcd Uploaded bgruening parents: diff changeset	201
2ad3b027dfcd Uploaded bgruening parents: diff changeset	202
2ad3b027dfcd Uploaded bgruening parents: diff changeset	203 You can find more details on the bamCorrelate wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamCorrelate
2ad3b027dfcd Uploaded bgruening parents: diff changeset	204
2ad3b027dfcd Uploaded bgruening parents: diff changeset	205
2ad3b027dfcd Uploaded bgruening parents: diff changeset	206 Output files:
2ad3b027dfcd Uploaded bgruening parents: diff changeset	207
2ad3b027dfcd Uploaded bgruening parents: diff changeset	208 - diagnostic plot: clustered heatmap displaying the values for each pair-wise correlation, see below for an example
2ad3b027dfcd Uploaded bgruening parents: diff changeset	209 - data matrix (optional): if you want to plot the correlation values using a different program, e.g. R, this matrix can be used
2ad3b027dfcd Uploaded bgruening parents: diff changeset	210
2ad3b027dfcd Uploaded bgruening parents: diff changeset	211
2ad3b027dfcd Uploaded bgruening parents: diff changeset	212 -----
2ad3b027dfcd Uploaded bgruening parents: diff changeset	213
2ad3b027dfcd Uploaded bgruening parents: diff changeset	214 @REFERENCES@
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	215 ]]>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	216 </help>
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	217 <expand macro="citations" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	218 </tool>

Mercurial > repos > bgruening > deeptools

annotate bamCorrelate.xml @ 30:5231f398d784 draft