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comparison bamCorrelate.xml @ 30:5231f398d784 draft

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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
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29:3a2aab18a217 30:5231f398d784
1 <tool id="deeptools_bamCorrelate" name="bamCorrelate" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_bamCorrelate" name="bamCorrelate" version="@WRAPPER_VERSION@.0">
2 <description>correlates pairs of BAM files</description> 2 <description>correlates pairs of BAM files</description>
3 <expand macro="requirements" />
4 <expand macro="stdio" />
5 <macros> 3 <macros>
6 <token name="@BINARY@">bamCorrelate</token> 4 <token name="@BINARY@">bamCorrelate</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 #set files=[] 10 #set files=[]
11 #set labels=[] 11 #set labels=[]
12 12
13 @multiple_input_bams@ 13 @multiple_input_bams@
14 14
16 16
17 $mode.modeOpt 17 $mode.modeOpt
18 18
19 @THREADS@ 19 @THREADS@
20 20
21 --bamfiles #echo " ".join($files) 21 --bamfiles '#echo "' '".join($files)#'
22 --labels #echo " ".join($labels) 22 --labels '#echo "' '".join($labels)#'
23 --fragmentLength $fragmentLength 23 --fragmentLength $fragmentLength
24 --corMethod $corMethod 24 --corMethod $corMethod
25 25
26 --plotFile $outFileName 26 --plotFile $outFileName
27 27
28 #if $output.showOutputSettings == "yes" 28 #if $output.showOutputSettings == "yes"
29 --outRawCounts '$outFileRawCounts' 29 --outRawCounts '$outFileRawCounts'
30 --outFileCorMatrix '$outFileCorMatrix' 30 --outFileCorMatrix '$outFileCorMatrix'
31 --plotFileFormat $output.outFileFormat 31 --plotFileFormat '$output.outFileFormat'
32 #else: 32 #else:
33 --plotFileFormat 'png' 33 --plotFileFormat 'png'
34 #end if 34 #end if
35 35
36 #if $mode.modeOpt == "bins": 36 #if $mode.modeOpt == "bins":
37 --binSize '$mode.binSize' 37 --binSize '$mode.binSize'
38 --distanceBetweenBins '$mode.distanceBetweenBins' 38 --distanceBetweenBins '$mode.distanceBetweenBins'
39 $mode.doNotRemoveOutliers 39 $mode.doNotRemoveOutliers
40
41 #else: 40 #else:
42 --BED $mode.region_file 41 --BED $mode.region_file
43 #end if 42 #end if
44 43
45 #### options available in both modes 44 #### options available in both modes
46 #if str($mode.region.value) != '': 45 #if str($mode.region.value) != '':
47 --region '$mode.region' 46 --region '$mode.region'
48 #end if 47 #end if
49 48
49 #if $plotTitle and str($plotTitle).strip() != "":
50 --plotTitle '$plotTitle'
51 #end if
52 $plotNumbers
50 #if $mode.advancedOpt.showAdvancedOpt == "yes": 53 #if $mode.advancedOpt.showAdvancedOpt == "yes":
51 54
52 $mode.advancedOpt.doNotExtendPairedEnds 55 $mode.advancedOpt.doNotExtendPairedEnds
53 $mode.advancedOpt.ignoreDuplicates 56 $mode.advancedOpt.ignoreDuplicates
54 $mode.advancedOpt.includeZeros 57 $mode.advancedOpt.includeZeros
64 --zMax $mode.advancedOpt.zMax 67 --zMax $mode.advancedOpt.zMax
65 #end if 68 #end if
66 --colorMap '$mode.advancedOpt.colorMap' 69 --colorMap '$mode.advancedOpt.colorMap'
67 70
68 #end if 71 #end if
72 ]]>
69 </command> 73 </command>
70 74
71 <inputs> 75 <inputs>
72 <expand macro="multiple_input_bams" /> 76 <expand macro="multiple_input_bams" />
73 77
74 <param name="fragmentLength" type="integer" value="300" min="1" 78 <param name="fragmentLength" type="integer" value="200" min="1"
75 label="Length of the average fragment size" 79 label="Length of the average fragment size"
76 help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/> 80 help ="Reads will be extended to match this length unless they are paired-end,
81 in which case they will be extended to match the fragment length.
82 *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will
83 be extended to match the fragment length. (--fragmentLength)"/>
77 84
78 <param name="corMethod" type="select" label="Correlation method"> 85 <param name="corMethod" type="select" label="Correlation method">
79 <option value="spearman" selected="True">Spearman</option> 86 <option value="spearman" selected="True">Spearman</option>
80 <option value="pearson">Pearson</option> 87 <option value="pearson">Pearson</option>
81 </param> 88 </param>
82 89
83 <conditional name="mode"> 90 <conditional name="mode">
84 <param name="modeOpt" type="select" label="Choose computation mode" 91 <param name="modeOpt" type="select" label="Choose computation mode"
85 help="In the bins mode, the correlation is computed based on equal length bins. In the BED file mode, as list of genomic regions in BED format has to be given. For each region in the BED file the number of overlapping reads is counted in each of the BAM files. Then the correlation is computed."> 92 help="In the bins mode, the correlation is computed based on equal
93 length bins. In the BED file mode, as list of genomic regions in BED
94 format has to be given. For each region in the BED file the number of
95 overlapping reads is counted in each of the BAM files.
96 Then the correlation is computed.">
86 <option value="bins" selected="true">Bins</option> 97 <option value="bins" selected="true">Bins</option>
87 <option value="BED-file">Limit correlation to certain regions (BED file)</option> 98 <option value="BED-file">Limit correlation to certain regions (BED file)</option>
88 </param> 99 </param>
89 <when value="bins"> 100 <when value="bins">
90 <param name="binSize" type="integer" value="10000" min="1" 101 <param name="binSize" type="integer" value="10000" min="1"
91 label="Bin size in bp" 102 label="Bin size in bp"
92 help="Length in base pairs for a window used to sample the genome."/> 103 help="Length in base pairs for a window used to sample the genome. (--binSize)"/>
93 104
94 <param name="distanceBetweenBins" type="integer" value="0" min="0" 105 <param name="distanceBetweenBins" type="integer" value="0" min="0"
95 label="Distance between bins" 106 label="Distance between bins"
96 help="By default, bamCorrelate considers consecutive bins of 107 help="By default, bamCorrelate considers consecutive bins of
97 the specified 'Bin size'. However, to reduce the 108 the specified 'Bin size'. However, to reduce the
98 computation time, a larger distance between bins can 109 computation time, a larger distance between bins can
99 by given. Larger distances result in less bins being 110 by given. Larger distances result in less bins being
100 considered"/> 111 considered. (--distanceBetweenBins)"/>
101 112
102 <param name="doNotRemoveOutliers" type="boolean" 113 <param name="doNotRemoveOutliers" type="boolean"
103 truevalue="--doNotRemoveOutliers" falsevalue="" label="Do not filter outliers" 114 truevalue="--doNotRemoveOutliers" falsevalue="" label="Do not filter outliers"
104 help="By default, bins with very large counts are removed. 115 help="By default, bins with very large counts are removed.
105 By setting this option, outliers will not be 116 By setting this option, outliers will not be
109 removed the pearson correlation will wrongly report a 120 removed the pearson correlation will wrongly report a
110 very high correlation; that's why, by default, 121 very high correlation; that's why, by default,
111 bamCorrelate tries to remove outliers using 122 bamCorrelate tries to remove outliers using
112 the median absolute deviation (MAD) method applying a 123 the median absolute deviation (MAD) method applying a
113 threshold of 200 to only consider extremely large 124 threshold of 200 to only consider extremely large
114 deviations from the median."/> 125 deviations from the median. (--doNotRemoveOutliers)"/>
115 126
116 <expand macro="bamCorrelate_mode_actions" /> 127 <expand macro="bamCorrelate_mode_actions" />
117 </when> 128 </when>
118 <when value="BED-file"> 129 <when value="BED-file">
119 <param name="region_file" type="data" format="bed" label="Region file in BED format" help="Correlation is computed for the number of reads that overlap such regions."/> 130 <param name="region_file" type="data" format="bed"
131 label="Region file in BED format"
132 help="Correlation is computed for the number of reads that overlap such regions."/>
120 <expand macro="bamCorrelate_mode_actions" /> 133 <expand macro="bamCorrelate_mode_actions" />
121 </when> 134 </when>
122
123 </conditional> 135 </conditional>
124 136 <expand macro="plotTitle" />
137 <expand macro="plotNumbers" />
125 <conditional name="output"> 138 <conditional name="output">
126 <param name="showOutputSettings" type="select" label="Show advanced output settings" > 139 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
127 <option value="no" selected="true">no</option> 140 <option value="no" selected="true">no</option>
128 <option value="yes">yes</option> 141 <option value="yes">yes</option>
129 </param> 142 </param>
153 output['saveCorMatrix'] is True 166 output['saveCorMatrix'] is True
154 )) 167 ))
155 </filter> 168 </filter>
156 </data> 169 </data>
157 </outputs> 170 </outputs>
171 <tests>
172 <test>
173 <repeat name="input_files">
174 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
175 <param name="label" value="first BAM file" />
176 </repeat>
177 <repeat name="input_files">
178 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
179 <param name="label" value="second BAM file" />
180 </repeat>
181 <param name="modeOpt" value="bins" />
182 <param name="binSize" value="10" />
183 <param name="showOutputSettings" value="no" />
184 <output name="outFileName" file="bamCorrelate_result1.png" ftype="png" compare="sim_size" />
185 </test>
186 </tests>
158 <help> 187 <help>
159 188 <![CDATA[
160 **What it does** 189 **What it does**
161 190
162 This tool is useful to assess the overall similarity of different BAM files. A typical application 191 This tool is useful to assess the overall similarity of different BAM files. A typical application
163 is to check the correlation between replicates or published data sets. 192 is to check the correlation between replicates or published data sets.
164 193
181 210
182 211
183 ----- 212 -----
184 213
185 @REFERENCES@ 214 @REFERENCES@
186 215 ]]>
187 </help> 216 </help>
188 <expand macro="citations" /> 217 <expand macro="citations" />
189 </tool> 218 </tool>