Mercurial > repos > bgruening > deeptools_plot_fingerprint

comparison plotFingerprint.xml @ 16:2768f00a7d25 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
author bgruening
date Mon, 05 Dec 2016 07:48:34 -0500
parents ea9198c920f6
children d0390db2a666
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15:5bc9d7f363a6 16:2768f00a7d25
17 #if $output.showOutputSettings == "yes" 17 #if $output.showOutputSettings == "yes"
18 --plotFileFormat $output.outFileFormat 18 --plotFileFormat $output.outFileFormat
19 #if $output.saveRawCounts: 19 #if $output.saveRawCounts:
20 --outRawCounts '$outFileRawCounts' 20 --outRawCounts '$outFileRawCounts'
21 #end if 21 #end if
22 #if $output.saveQualityMetrics:
23 --outQualityMetrics '$outFileQualityMetrics'
24 #if $output.JSDsample:
25 #if "'{}'".format($output.JSDsample.display_name) in $labels:
26 #set JSDidx = $labels.index("'{}'".format($output.JSDsample.display_name))
27 --JSDsample "./${JSDidx}.bam"
28 #end if
29 #end if
30 #end if
22 #else 31 #else
23 --plotFileFormat 'png' 32 --plotFileFormat 'png'
24 #end if 33 #end if
25 34
26 #if str($region).strip() != '': 35 #if str($region).strip() != '':
31 --binSize '$advancedOpt.binSize' 40 --binSize '$advancedOpt.binSize'
32 --numberOfSamples '$advancedOpt.numberOfSamples' 41 --numberOfSamples '$advancedOpt.numberOfSamples'
33 42
34 $advancedOpt.ignoreDuplicates 43 $advancedOpt.ignoreDuplicates
35 $advancedOpt.skipZeros 44 $advancedOpt.skipZeros
36
37 #if $advancedOpt.minMappingQuality:
38 --minMappingQuality '$advancedOpt.minMappingQuality'
39 #end if
40 45
41 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": 46 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
42 --plotTitle '$advancedOpt.plotTitle' 47 --plotTitle '$advancedOpt.plotTitle'
43 #end if 48 #end if
44 @ADVANCED_OPTS_READ_PROCESSING@ 49 @ADVANCED_OPTS_READ_PROCESSING@
78 </param> 83 </param>
79 <when value="no" /> 84 <when value="no" />
80 <when value="yes"> 85 <when value="yes">
81 <expand macro="input_image_file_format" /> 86 <expand macro="input_image_file_format" />
82 <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/> 87 <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/>
88 <param name="saveQualityMetrics" type="boolean" label="Save quality metrics"
89 help="The file will have one row per input BAM file and columns containing a variety of QC metrics. For the full description of all metrics and their interpretation, please see our online documentation: http://deeptools.readthedocs.io/en/latest/content/feature/plotFingerprint_QC_metrics.html. (--outQualityMetrics)"/>
90 <param name="JSDsample" type="data" format="bam"
91 label="Jensen-Shannon distance reference sample"
92 help="If output metrics should be saved, then use this sample as the reference for computing the Jensen-Shannon distance and CHANCE metrics of all other samples. Normally this is an input sample. If you don't specify this, then these metrics will not be computed. This is only applicable if quality metrics are being saved. (--JSDsample)" />
83 </when> 93 </when>
84 </conditional> 94 </conditional>
85 </inputs> 95 </inputs>
86 <outputs> 96 <outputs>
87 <expand macro="output_image_file_format" /> 97 <expand macro="output_image_file_format" />
88 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> 98 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
89 <filter> 99 <filter>
90 (( 100 ((
91 output['showOutputSettings'] == 'yes' and 101 output['showOutputSettings'] == 'yes' and
92 output['saveRawCounts'] is True 102 output['saveRawCounts'] is True
103 ))
104 </filter>
105 </data>
106 <data format="tabular" name="outFileQualityMetrics" label="${tool.name} on ${on_string}: quality metrics">
107 <filter>
108 ((
109 output['showOutputSettings'] == 'yes' and
110 output['saveQualityMetrics'] is True
93 )) 111 ))
94 </filter> 112 </filter>
95 </data> 113 </data>
96 </outputs> 114 </outputs>
97 <tests> 115 <tests>
104 <test> 122 <test>
105 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" /> 123 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
106 <param name="showAdvancedOpt" value="yes" /> 124 <param name="showAdvancedOpt" value="yes" />
107 <param name="showOutputSettings" value="yes" /> 125 <param name="showOutputSettings" value="yes" />
108 <param name="saveRawCounts" value="True" /> 126 <param name="saveRawCounts" value="True" />
127 <param name="saveQualityMetrics" value="True" />
109 <param name="plotTitle" value="Test Fingerprint Plot" /> 128 <param name="plotTitle" value="Test Fingerprint Plot" />
129 <param name="JSDsample" value="bowtie2 test1.bam" ftype="bam" />
110 <output name="outFileName" file="plotFingerprint_result2.png" ftype="png" compare="sim_size" /> 130 <output name="outFileName" file="plotFingerprint_result2.png" ftype="png" compare="sim_size" />
111 <output name="outFileRawCounts" file="plotFingerprint_result2.tabular" ftype="tabular" /> 131 <output name="outFileRawCounts" file="plotFingerprint_result2.tabular" ftype="tabular" />
132 <output name="outFileQualityMetrics" file="plotFingerprint_quality_metrics.tabular" ftype="tabular" />
112 </test> 133 </test>
113 </tests> 134 </tests>
114 <help> 135 <help>
115 <![CDATA[ 136 <![CDATA[
116 137
125 Output 146 Output
126 ------ 147 ------
127 148
128 The default output is a diagnostic plot (see below for an example and further down for some background information). 149 The default output is a diagnostic plot (see below for an example and further down for some background information).
129 150
130 Optionally, you can obtain the table of raw counts that was used to generate the plot. 151 Optionally, you can obtain the table of raw values that were used to generate the plot.
131 152
132 .. image:: $PATH_TO_IMAGES/plotFingerprint_output.png 153 .. image:: $PATH_TO_IMAGES/plotFingerprint_output.png
133 :width: 600 154 :width: 600
134 :height: 395 155 :height: 395
135 156
147 ----- 168 -----
148 169
149 Theoretical Background 170 Theoretical Background
150 ---------------------- 171 ----------------------
151 172
152 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of the specified length. 173 The tool first samples indexed BAM files and sums the per-base coverage of reads/fragments overlapping a window (bin) of the specified length.
153 These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank) 174 These values are then sorted according to their rank (the bin with the highest number of reads has the highest rank)
154 and the cumulative sum of read counts are plotted. An ideal input (control) with a uniform distribution of reads alignments 175 and the cumulative sum plotted. An ideal input (control) with a uniform distribution of reads alignments
155 result in a diagonal line. A very specific and strong ChIP enrichment, on the other hand, would result in a large portion 176 and infinite sequencing depth will result in a diagonal line. A very specific and strong ChIP enrichment, on the other hand, would result in a large portion
156 of reads accumulating in just a few bins and the resulting plot showing a steep rise toward the right-most edge. Such results are 177 of reads accumulating in just a few bins and the resulting plot showing a steep rise toward the right-most edge. Such results are
157 most commonly seen with transcription factors. 178 most commonly seen with transcription factors.
158 179
159 180
160 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png 181 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png