Mercurial > repos > bgruening > deeptools

comparison bamFingerprint.xml @ 30:5231f398d784 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
29:3a2aab18a217 30:5231f398d784
1 <tool id="deeptools_bamFingerprint" name="bamFingerprint" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_bamFingerprint" name="bamFingerprint" version="@WRAPPER_VERSION@.0">
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" />
4 <expand macro="stdio" />
5 <macros> 3 <macros>
6 <token name="@BINARY@">bamFingerprint</token> 4 <token name="@BINARY@">bamFingerprint</token>
7 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
8 </macros> 6 </macros>
7 <expand macro="requirements" />
9 <command> 8 <command>
9 <![CDATA[
10 @multiple_input_bams@ 10 @multiple_input_bams@
11 11
12 bamFingerprint 12 bamFingerprint
13 13
14 @THREADS@ 14 @THREADS@
15 15
16 --bamfiles #echo " ".join($files) 16 --bamfiles #echo " ".join($files)
17 --labels #echo " ".join($labels) 17 --labels #echo " ".join($labels)
18 18
19 --fragmentLength $fragmentLength 19 --fragmentLength $fragmentLength
20 20
21 #set newoutFileName=str($outFileName)+".png" 21 --plotFile $outFileName
22 --plotFile $newoutFileName
23 22
24 #if $output.showOutputSettings == "yes" 23 #if $output.showOutputSettings == "yes"
25 --plotFileFormat $output.outFileFormat 24 --plotFileFormat $output.outFileFormat
26 #if $output.saveRawCounts: 25 #if $output.saveRawCounts:
27 --outRawCounts '$outFileRawCounts' 26 --outRawCounts '$outFileRawCounts'
28 #end if 27 #end if
29 #else 28 #else
30 --plotFileFormat 'png' 29 --plotFileFormat 'png'
31 #end if 30 #end if
32 31
33 #if str($region).strip() != '': 32 #if str($region).strip() != '':
34 --region '$region' 33 --region '$region'
35 #end if 34 #end if
36 35
37 #if $advancedOpt.showAdvancedOpt == "yes": 36 #if $advancedOpt.showAdvancedOpt == "yes":
38 --binSize '$advancedOpt.binSize' 37 --binSize '$advancedOpt.binSize'
39 --numberOfSamples '$advancedOpt.numberOfSamples' 38 --numberOfSamples '$advancedOpt.numberOfSamples'
40 39
41 $advancedOpt.doNotExtendPairedEnds 40 $advancedOpt.doNotExtendPairedEnds
42 $advancedOpt.ignoreDuplicates 41 $advancedOpt.ignoreDuplicates
43 $advancedOpt.skipZeros 42 $advancedOpt.skipZeros
44 43
45 #if $advancedOpt.minMappingQuality: 44 #if $advancedOpt.minMappingQuality:
46 --minMappingQuality '$advancedOpt.minMappingQuality' 45 --minMappingQuality '$advancedOpt.minMappingQuality'
47 #end if 46 #end if
48 #end if 47
49 ; mv $newoutFileName $outFileName 48 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
50 ; rm $temp_dir -rf 49 --plotTitle '$advancedOpt.plotTitle'
50 #end if
51
52 #end if
53 ]]>
51 </command> 54 </command>
52 55
53 <inputs> 56 <inputs>
54 <expand macro="multiple_input_bams" /> 57 <expand macro="multiple_input_bams" />
55 58 <expand macro="fragmentLength" />
56
57 <param name="fragmentLength" type="integer" value="200" min="1"
58 label="Length of the average fragment size"/>
59
60 <expand macro="region_limit_operation" /> 59 <expand macro="region_limit_operation" />
61 60
62 <conditional name="advancedOpt"> 61 <conditional name="advancedOpt">
63 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 62 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
64 <option value="no" selected="true">no</option> 63 <option value="no" selected="true">no</option>
65 <option value="yes">yes</option> 64 <option value="yes">yes</option>
66 </param> 65 </param>
67 <when value="no" /> 66 <when value="no" />
68 <when value="yes"> 67 <when value="yes">
69 <param name="binSize" type="integer" value="10000" min="1" 68 <param name="binSize" type="integer" value="500" min="1"
70 label="Bin size in bp" 69 label="Bin size in bp"
71 help="Length in base pairs for a window used to sample the genome."/> 70 help="Length in base pairs for a window used to sample the genome."/>
72
73 <param name="numberOfSamples" type="integer" value="100000" min="1" 71 <param name="numberOfSamples" type="integer" value="100000" min="1"
74 label="Number of samples" 72 label="Number of samples"
75 help="Number of samples taken from the genome to compute the scaling factors"/> 73 help="Number of samples taken from the genome to compute the scaling factors. (--numberOfSamples)"/>
76 74 <expand macro="doNotExtendPairedEnds" />
77 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" 75 <expand macro="ignoreDuplicates" />
78 label="Do not extend paired ends" 76 <expand macro="minMappingQuality" />
79 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/> 77 <expand macro="skipZeros" />
80 78 <expand macro="plotTitle" />
81 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
82 label="Ignore duplicates"
83 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
84
85 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
86 label="Minimum mapping quality"
87 help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
88
89 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
90 label ="Include zeros"
91 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined." />
92 </when> 79 </when>
93 </conditional> 80 </conditional>
94
95 <conditional name="output"> 81 <conditional name="output">
96 <param name="showOutputSettings" type="select" label="Show advanced output settings"> 82 <param name="showOutputSettings" type="select" label="Show advanced output settings">
97 <option value="no" selected="true">no</option> 83 <option value="no" selected="true">no</option>
98 <option value="yes">yes</option> 84 <option value="yes">yes</option>
99 </param> 85 </param>
100 <when value="no" /> 86 <when value="no" />
101 <when value="yes"> 87 <when value="yes">
102 <expand macro="input_image_file_format" /> 88 <expand macro="input_image_file_format" />
103 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/> 89 <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/>
104 </when> 90 </when>
105 </conditional> 91 </conditional>
106
107 </inputs> 92 </inputs>
108 <outputs> 93 <outputs>
109 <expand macro="output_image_file_format" /> 94 <expand macro="output_image_file_format" />
110 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> 95 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
111 <filter> 96 <filter>
114 output['saveRawCounts'] is True 99 output['saveRawCounts'] is True
115 )) 100 ))
116 </filter> 101 </filter>
117 </data> 102 </data>
118 </outputs> 103 </outputs>
104 <tests>
105 <test>
106 <repeat name="input_files">
107 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
108 </repeat>
109 <repeat name="input_files">
110 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
111 </repeat>
112 <param name="fragmentLength" value="200" />
113 <param name="showAdvancedOpt" value="no" />
114 <param name="showOutputSettings" value="no" />
115 <output name="outFileName" file="bamFingerprint_result1.png" ftype="png" compare="sim_size" />
116 </test>
117 </tests>
119 <help> 118 <help>
120 119 <![CDATA[
121 **What it does** 120 **What it does**
122 121
123 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) 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)
124 and it is based on a method developed by Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3). 123 and it is based on a method developed by Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
125 124
144 - Data matrix of raw counts 143 - Data matrix of raw counts
145 144
146 ----- 145 -----
147 146
148 @REFERENCES@ 147 @REFERENCES@
149 148 ]]>
150 </help> 149 </help>
151 <expand macro="citations" /> 150 <expand macro="citations" />
152 </tool> 151 </tool>