deeptools: bamFingerprint.xml annotate

annotate bamFingerprint.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_bamFingerprint" name="bamFingerprint" version="@WRAPPER_VERSION@.0">
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	2 <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	3 <macros>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	4 <token name="@BINARY@">bamFingerprint</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 @multiple_input_bams@
2ad3b027dfcd Uploaded bgruening parents: diff changeset	11
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	12 bamFingerprint
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	13
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	14 @THREADS@
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	15
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	16 --bamfiles #echo " ".join($files)
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	17 --labels #echo " ".join($labels)
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	18
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	19 --fragmentLength $fragmentLength
26 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 --plotFile $outFileName
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	22
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	23 #if $output.showOutputSettings == "yes"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	24 --plotFileFormat $output.outFileFormat
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	25 #if $output.saveRawCounts:
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	26 --outRawCounts '$outFileRawCounts'
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	27 #end if
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	28 #else
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	29 --plotFileFormat 'png'
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	30 #end if
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	31
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	32 #if str($region).strip() != '':
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	33 --region '$region'
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	34 #end if
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 $advancedOpt.showAdvancedOpt == "yes":
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	37 --binSize '$advancedOpt.binSize'
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	38 --numberOfSamples '$advancedOpt.numberOfSamples'
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	39
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	40 $advancedOpt.doNotExtendPairedEnds
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	41 $advancedOpt.ignoreDuplicates
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	42 $advancedOpt.skipZeros
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	43
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	44 #if $advancedOpt.minMappingQuality:
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	45 --minMappingQuality '$advancedOpt.minMappingQuality'
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	46 #end if
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	47
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	48 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	49 --plotTitle '$advancedOpt.plotTitle'
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
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	51
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	52 #end if
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	53 ]]>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	54 </command>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	55
2ad3b027dfcd Uploaded bgruening parents: diff changeset	56 <inputs>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	57 <expand macro="multiple_input_bams" />
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	58 <expand macro="fragmentLength" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	59 <expand macro="region_limit_operation" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	60
2ad3b027dfcd Uploaded bgruening parents: diff changeset	61 <conditional name="advancedOpt">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	62 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
2ad3b027dfcd Uploaded bgruening parents: diff changeset	63 <option value="no" selected="true">no</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	64 <option value="yes">yes</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	65 </param>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	66 <when value="no" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	67 <when value="yes">
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	68 <param name="binSize" type="integer" value="500" min="1"
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	69 label="Bin size in bp"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	70 help="Length in base pairs for a window used to sample the genome."/>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	71 <param name="numberOfSamples" type="integer" value="100000" min="1"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	72 label="Number of samples"
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	73 help="Number of samples taken from the genome to compute the scaling factors. (--numberOfSamples)"/>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	74 <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	75 <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	76 <expand macro="minMappingQuality" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	77 <expand macro="skipZeros" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	78 <expand macro="plotTitle" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	79 </when>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	80 </conditional>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	81 <conditional name="output">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	82 <param name="showOutputSettings" type="select" label="Show advanced output settings">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	83 <option value="no" selected="true">no</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	84 <option value="yes">yes</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	85 </param>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	86 <when value="no" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	87 <when value="yes">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	88 <expand macro="input_image_file_format" />
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	89 <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	90 </when>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	91 </conditional>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	92 </inputs>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	93 <outputs>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	94 <expand macro="output_image_file_format" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	95 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	96 <filter>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	97 ((
2ad3b027dfcd Uploaded bgruening parents: diff changeset	98 output['showOutputSettings'] == 'yes' and
2ad3b027dfcd Uploaded bgruening parents: diff changeset	99 output['saveRawCounts'] is True
2ad3b027dfcd Uploaded bgruening parents: diff changeset	100 ))
2ad3b027dfcd Uploaded bgruening parents: diff changeset	101 </filter>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	102 </data>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	103 </outputs>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	104 <tests>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	105 <test>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	106 <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	107 <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	108 </repeat>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	109 <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	110 <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	111 </repeat>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	112 <param name="fragmentLength" value="200" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	113 <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	114 <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	115 <output name="outFileName" file="bamFingerprint_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	116 </test>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	117 </tests>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	118 <help>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	119 <![CDATA[
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	120 What it does
2ad3b027dfcd Uploaded bgruening parents: diff changeset	121
2ad3b027dfcd Uploaded bgruening parents: diff changeset	122 This tool is useful to assess the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background signal)
2ad3b027dfcd Uploaded bgruening parents: diff changeset	123 and it is based on a method developed by Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
2ad3b027dfcd Uploaded bgruening parents: diff changeset	124
2ad3b027dfcd Uploaded bgruening parents: diff changeset	125 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of specified length.
2ad3b027dfcd Uploaded bgruening parents: diff changeset	126 These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank)
2ad3b027dfcd Uploaded bgruening parents: diff changeset	127 and the cumulative sum of read counts are plotted. An ideal input (control sample) with perfect uniform distribution of reads
2ad3b027dfcd Uploaded bgruening parents: diff changeset	128 along the genome (i.e. without enrichments in open chromatin etc.) should
2ad3b027dfcd Uploaded bgruening parents: diff changeset	129 generate a straight diagonal line. A very specific and strong ChIP enrichment will be indicated by a prominent and steep
2ad3b027dfcd Uploaded bgruening parents: diff changeset	130 rise of the cumulative sum towards the highest rank. This means that a big chunk of reads from the ChIP sample is located in
2ad3b027dfcd Uploaded bgruening parents: diff changeset	131 few bins which corresponds to high, narrow enrichments seen for transcription factors.
2ad3b027dfcd Uploaded bgruening parents: diff changeset	132
2ad3b027dfcd Uploaded bgruening parents: diff changeset	133
2ad3b027dfcd Uploaded bgruening parents: diff changeset	134 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
2ad3b027dfcd Uploaded bgruening parents: diff changeset	135
2ad3b027dfcd Uploaded bgruening parents: diff changeset	136
2ad3b027dfcd Uploaded bgruening parents: diff changeset	137 You can find more details on the bamFingerprint wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint
2ad3b027dfcd Uploaded bgruening parents: diff changeset	138
2ad3b027dfcd Uploaded bgruening parents: diff changeset	139
2ad3b027dfcd Uploaded bgruening parents: diff changeset	140 Output files:
2ad3b027dfcd Uploaded bgruening parents: diff changeset	141
2ad3b027dfcd Uploaded bgruening parents: diff changeset	142 - Diagnostic plot
2ad3b027dfcd Uploaded bgruening parents: diff changeset	143 - Data matrix of raw counts
2ad3b027dfcd Uploaded bgruening parents: diff changeset	144
2ad3b027dfcd Uploaded bgruening parents: diff changeset	145 -----
2ad3b027dfcd Uploaded bgruening parents: diff changeset	146
2ad3b027dfcd Uploaded bgruening parents: diff changeset	147 @REFERENCES@
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	148 ]]>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	149 </help>
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	150 <expand macro="citations" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	151 </tool>

Mercurial > repos > bgruening > deeptools

annotate bamFingerprint.xml @ 30:5231f398d784 draft