Mercurial > repos > bgruening > deeptools
comparison bamFingerprint.xml @ 18:5ea8782d650c draft
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author | bgruening |
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date | Mon, 03 Feb 2014 13:44:35 -0500 |
parents | 16310f8b24d5 |
children | 69ff16ba27bd |
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17:ef65d6b68ccc | 18:5ea8782d650c |
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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 "chr10" or "chr10:456700:891000"" /> | |
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> |