Mercurial > repos > bgruening > deeptools

comparison bamCorrelate.xml @ 18:5ea8782d650c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Mon, 03 Feb 2014 13:44:35 -0500
parents 16310f8b24d5
children 8c452f37c896
comparison
equal deleted inserted replaced
17:ef65d6b68ccc 18:5ea8782d650c
1 <tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.2"> 1 <tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.3">
2 <description>correlates pairs of BAM files</description> 2 <description>correlates pairs of BAM files</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <expand macro="stdio" /> 4 <expand macro="stdio" />
5 <macros> 5 <macros>
6 <token name="@BINARY@">bamCorrelate</token>
6 <import>deepTools_macros.xml</import> 7 <import>deepTools_macros.xml</import>
7 </macros> 8 </macros>
8 <command> 9 <command>
9 #set files=[] 10 #set files=[]
10 #set labels=[] 11 #set labels=[]
37 --numberOfSamples '$mode.numberOfSamples' 38 --numberOfSamples '$mode.numberOfSamples'
38 #else: 39 #else:
39 --BED $mode.region_file 40 --BED $mode.region_file
40 #end if 41 #end if
41 42
42 ## options available in both modes 43 #### options available in both modes
44 #if str($mode.region.value) != '':
45 --region '$mode.region'
46 #end if
47
43 #if $mode.advancedOpt.showAdvancedOpt == "yes": 48 #if $mode.advancedOpt.showAdvancedOpt == "yes":
44
45 #if str($mode.advancedOpt.region.value) != '':
46 --region '$mode.advancedOpt.region'
47 #end if
48 49
49 $mode.advancedOpt.doNotExtendPairedEnds 50 $mode.advancedOpt.doNotExtendPairedEnds
50 $mode.advancedOpt.ignoreDuplicates 51 $mode.advancedOpt.ignoreDuplicates
51 $mode.advancedOpt.includeZeros 52 $mode.advancedOpt.includeZeros
52 53
147 148
148 .. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png 149 .. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png
149 :alt: Heatmap of RNA Polymerase II ChIP-seq 150 :alt: Heatmap of RNA Polymerase II ChIP-seq
150 151
151 152
153 You can find more details in the `bamCorrelate wiki`_.
154
155 .. _bamCorrelate wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
156
157
152 **Output files**: 158 **Output files**:
153 159
154 - diagnostic plot produced by bamCorrelate is a clustered heatmap displaying the values for each pair-wise correlation, see below for an example 160 - diagnostic plot produced by bamCorrelate is a clustered heatmap displaying the values for each pair-wise correlation, see below for an example
155 - data matrix (optional) in case you want to plot the correlation values using a different program, e.g. R, this matrix can be used 161 - data matrix (optional) in case you want to plot the correlation values using a different program, e.g. R, this matrix can be used
156 162
157 163
158
159
160 ----- 164 -----
161
162 .. class:: infomark
163 165
164 @REFERENCES@ 166 @REFERENCES@
165 167
166 </help> 168 </help>
167 </tool> 169 </tool>