comparison bamFingerprint.xml @ 18:5ea8782d650c draft

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author bgruening
date Mon, 03 Feb 2014 13:44:35 -0500
parents 16310f8b24d5
children 69ff16ba27bd
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17:ef65d6b68ccc 18:5ea8782d650c
1 <tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0.2"> 1 <tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0.3">
2 <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description> 2 <description>plots profiles of BAM files; useful for assesing ChIP signal strength</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@">bamFingerprint</token>
6 <import>deepTools_macros.xml</import> 7 <import>deepTools_macros.xml</import>
7 </macros> 8 </macros>
8 <command> 9 <command>
9 @multiple_input_bams@ 10 @multiple_input_bams@
10 11
27 #end if 28 #end if
28 #else 29 #else
29 --plotFileFormat 'png' 30 --plotFileFormat 'png'
30 #end if 31 #end if
31 32
33 #if str(region).strip() != '':
34 --region 'region'
35 #end if
36
32 #if $advancedOpt.showAdvancedOpt == "yes": 37 #if $advancedOpt.showAdvancedOpt == "yes":
33
34 #if str($advancedOpt.region.value) != '':
35 --region '$advancedOpt.region'
36 #end if
37
38 --binSize '$advancedOpt.binSize' 38 --binSize '$advancedOpt.binSize'
39 --numberOfSamples '$advancedOpt.numberOfSamples' 39 --numberOfSamples '$advancedOpt.numberOfSamples'
40 40
41 $advancedOpt.doNotExtendPairedEnds 41 $advancedOpt.doNotExtendPairedEnds
42 $advancedOpt.ignoreDuplicates 42 $advancedOpt.ignoreDuplicates
51 </command> 51 </command>
52 52
53 <inputs> 53 <inputs>
54 <expand macro="multiple_input_bams" /> 54 <expand macro="multiple_input_bams" />
55 55
56
56 <param name="fragmentLength" type="integer" value="200" min="1" 57 <param name="fragmentLength" type="integer" value="200" min="1"
57 label="Length of the average fragment size"/> 58 label="Length of the average fragment size"/>
59
60 <expand macro="region_limit_operation" />
61
58 <conditional name="advancedOpt"> 62 <conditional name="advancedOpt">
59 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 63 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
60 <option value="no" selected="true">no</option> 64 <option value="no" selected="true">no</option>
61 <option value="yes">yes</option> 65 <option value="yes">yes</option>
62 </param> 66 </param>
63 <when value="no" /> 67 <when value="no" />
64 <when value="yes"> 68 <when value="yes">
65 <param name="region" type="text" value=""
66 label="Region of the genome to limit the operation to"
67 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
68
69 <param name="binSize" type="integer" value="10000" min="1" 69 <param name="binSize" type="integer" value="10000" min="1"
70 label="Bin size in bp" 70 label="Bin size in bp"
71 help="Length in base pairs for a window used to sample the genome."/> 71 help="Length in base pairs for a window used to sample the genome."/>
72 72
73 <param name="numberOfSamples" type="integer" value="100000" min="1" 73 <param name="numberOfSamples" type="integer" value="100000" min="1"
131 131
132 132
133 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png 133 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
134 134
135 135
136 You can find more details in the `bamFingerprint wiki`_.
137
138 .. _bamFingerprint wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint
139
140
136 **Output files**: 141 **Output files**:
137 142
138 - Diagnostic plot 143 - Diagnostic plot
139 - Data matrix of raw counts 144 - Data matrix of raw counts
140 145
141 ----- 146 -----
142 147
143 .. class:: infomark
144
145 @REFERENCES@ 148 @REFERENCES@
146 149
147 </help> 150 </help>
148 </tool> 151 </tool>