Mercurial > repos > bgruening > deeptools_bam_pe_fragmentsize

comparison bamPEFragmentSize.xml @ 17:68932756bf49 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
author bgruening
date Thu, 15 Feb 2018 05:20:11 -0500
parents 4885b33dba09
children f011488450e6
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16:10ef0a306a46 17:68932756bf49
1 <tool id="deeptools_bam_pe_fragmentsize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_bam_pe_fragmentsize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0">
2 <description>Estimate the predominant cDNA fragment length from paired-end sequenced BAM files</description> 2 <description>Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">bamPEFragmentSize</token> 4 <token name="@BINARY@">bamPEFragmentSize</token>
5 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
15 --samplesLabel #echo " ".join($samplesLabel) 15 --samplesLabel #echo " ".join($samplesLabel)
16 #else: 16 #else:
17 --samplesLabel #echo " ".join($labels) 17 --samplesLabel #echo " ".join($labels)
18 #end if 18 #end if
19 #if $histogram: 19 #if $histogram:
20 --histogram ./hist.png 20 --histogram '$histogram_outfile'
21 --plotFileFormat '$outFileFormat'
21 #end if 22 #end if
22 --plotTitle "$plotTitle" 23 --plotTitle "$plotTitle"
23 #if $advancedOpt.showAdvancedOpt == 'yes' 24 #if $advancedOpt.showAdvancedOpt == 'yes'
24 --binSize '$advancedOpt.binSize' 25 --binSize '$advancedOpt.binSize'
25 --distanceBetweenBins '$advancedOpt.distanceBetweenBins' 26 --distanceBetweenBins '$advancedOpt.distanceBetweenBins'
26 $advancedOpt.logScale 27 $advancedOpt.logScale
27 --maxFragmentLength '$advancedOpt.maxFragmentLength' 28 --maxFragmentLength '$advancedOpt.maxFragmentLength'
28 @blacklist@ 29 @blacklist@
30 #if $advancedOpt.table
31 --table '$table'
32 #end if
33 #if $advancedOpt.outRawFragmentLengths
34 --outRawFragmentLengths '$fragLengths'
35 #end if
29 #end if 36 #end if
30 > $outfile 37 > '$outfile'
31 ]]> 38 ]]>
32 </command> 39 </command>
33 <inputs> 40 <inputs>
34 <expand macro="multiple_input_bams" MIN="1" /> 41 <expand macro="multiple_input_bams" MIN="1" />
35 <param argument="--histogram" type="boolean" truevalue="--histogram" falsevalue="" 42 <param argument="--histogram" type="boolean" truevalue="--histogram" falsevalue=""
36 label="Get the distribution of fragment lengths as a histogram" 43 label="Get the distribution of read/fragment lengths as a histogram"
37 help=""/> 44 help=""/>
45 <expand macro="input_image_file_format" />
38 <param argument="--samplesLabel" type="text" size="30" 46 <param argument="--samplesLabel" type="text" size="30"
39 label="Labels for the samples (each BAM file) plotted" 47 label="Labels for the samples (each BAM file) plotted"
40 help="The default is to use the file name of the sample. The sample labels should be separated by 48 help="The default is to use the file name of the sample. The sample labels should be separated by
41 spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;"> 49 spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
42 <sanitizer> 50 <sanitizer>
55 <param argument="--binSize" type="integer" value="1000" min="1" optional="true" 63 <param argument="--binSize" type="integer" value="1000" min="1" optional="true"
56 label="bin size, in bases" help="Length in bases of the window used to sample the genome. (--binSize)"/> 64 label="bin size, in bases" help="Length in bases of the window used to sample the genome. (--binSize)"/>
57 <param argument="--distanceBetweenBins" type="integer" value="1000000" min="0" optional="true" 65 <param argument="--distanceBetweenBins" type="integer" value="1000000" min="0" optional="true"
58 label="bin spacing, in bases" 66 label="bin spacing, in bases"
59 help="To reduce the computation time, not every possible genomic bin is sampled. This option allows you to set the distance between bins actually sampled from. Larger numbers are sufficient for high coverage samples, while smaller values are useful for lower coverage samples. Note that if you specify a value that results in too few (&lt;1000) reads sampled, the value will be decreased. (--distanceBetweenBins)"/> 67 help="To reduce the computation time, not every possible genomic bin is sampled. This option allows you to set the distance between bins actually sampled from. Larger numbers are sufficient for high coverage samples, while smaller values are useful for lower coverage samples. Note that if you specify a value that results in too few (&lt;1000) reads sampled, the value will be decreased. (--distanceBetweenBins)"/>
68 <param argument="--table" type="boolean" truevalue="--table" falsevalue=""
69 label="Write metrics to a tab-separated file?"
70 help="Write the read/fragment metrics to a tab-separated file, which is primarily useful for more automated downstream processing." />
71 <param argument="--outRawFragmentLengths" type="boolean" truevalue="--outRawFragmentLengths" falsevalue=""
72 label="Write a file containing the read/fragment length information?"
73 help="Write the read/fragment length distribution underlying the (optional) plot to a file. This can then be processed in R or other downstream applications." />
60 <param argument="--logScale" type="boolean" truevalue="--logScale" falsevalue="" 74 <param argument="--logScale" type="boolean" truevalue="--logScale" falsevalue=""
61 label="Plot log frequencies" 75 label="Plot log frequencies"
62 help="Plot the frequencies on the log10 scale" /> 76 help="Plot the frequencies on the log10 scale" />
63 77
64 <param argument="--maxFragmentLength" type="integer" min="0" value="0" 78 <param argument="--maxFragmentLength" type="integer" min="0" value="0"
68 </when> 82 </when>
69 </conditional> 83 </conditional>
70 84
71 </inputs> 85 </inputs>
72 <outputs> 86 <outputs>
73 <data name="outfile" format="txt"/> 87 <data name="outfile" format="txt" label="${tool.name} on ${on_string}: Read/Fragment metrics"/>
74 <data name="histogram_outfile" from_work_dir="hist.png" format="png"> 88 <data name="histogram_outfile" format="png" label="${tool.name} on ${on_string}: Read/Fragment histogram">
75 <filter>histogram is True</filter> 89 <filter>histogram is True</filter>
90 <change_format>
91 <when input="outFileFormat" value="pdf" format="pdf" />
92 <when input="outFileFormat" value="svg" format="svg" />
93 <when input="outFileFormat" value="eps" format="eps" />
94 <when input="outFileFormat" value="plotly" format="html" />
95 </change_format>
96 </data>
97 <data name="table" format="tabular" label="${tool.name} on ${on_string}: Read/Fragment metrics in tabular format">
98 <filter>table is True</filter>
99 </data>
100 <data name="fragLengths" format="tabular" label="${tool.name} on ${on_string}: Raw Read/Fragment lengths occurrences">
101 <filter>outRawFragmentLengths is True</filter>
76 </data> 102 </data>
77 </outputs> 103 </outputs>
78 <tests> 104 <tests>
79 <test> 105 <test>
80 <param name="bamfiles" value="bowtie2 test1.bam" ftype="bam" /> 106 <param name="bamfiles" value="bowtie2 test1.bam" ftype="bam" />
81 <param name="histogram" value="True" /> 107 <param name="histogram" value="True" />
82 <param name="plotTitle" value="Test Plot" /> 108 <param name="plotTitle" value="Test Plot" />
83 <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" /> 109 <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" />
84 <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size" /> 110 <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size" />
111 </test>
112 <test>
113 <param name="bamfiles" value="bowtie2 test1.bam" ftype="bam" />
114 <param name="showAdvancedOpt" value="yes" />
115 <param name="table" value="True" />
116 <param name="outRawFragmentLengths" value="yes" />
117 <output name="table" file="bamPEFragmentSize_table1.txt" ftype="tabular" />
118 <output name="fragLengths" file="bamPEFragmentSize_lengths1.txt" ftype="tabular" />
85 </test> 119 </test>
86 </tests> 120 </tests>
87 <help> 121 <help>
88 <![CDATA[ 122 <![CDATA[
89 123
102 136
103 .. image:: $PATH_TO_IMAGES/bamPEFragmentSize_output.png 137 .. image:: $PATH_TO_IMAGES/bamPEFragmentSize_output.png
104 :width: 600 138 :width: 600
105 :height: 520 139 :height: 520
106 140
141 If the ``--table`` option is specified, the summary statistics are additionally printed in a tabular format::
142
143 Frag. Len. Min. Frag. Len. 1st. Qu. Frag. Len. Mean Frag. Len. Median Frag. Len. 3rd Qu. Frag. Len. Max Frag. Len. Std. Read Len. Min. Read Len. 1st. Qu. Read Len. Mean Read Len. Median Read Len. 3rd Qu. Read Len. Max Read Len. Std.
144 bowtie2 test1.bam 241.0 241.5 244.666666667 242.0 246.5 251.0 4.49691252108 251.0 251.0 251.0 251.0 251.0 251.0 0.0
145
146 If the ``--outRawFragmentLengths`` option is provided, another history item will be produced, containing the raw data underlying the histogram. It has the following format::
147
148 #bamPEFragmentSize
149 Size Occurrences Sample
150 241 1 bowtie2 test1.bam
151 242 1 bowtie2 test1.bam
152 251 1 bowtie2 test1.bam
153
154 The "Size" is the fragment (or read, for single-end datasets) size and "Occurrences" are the number of times reads/fragments with that length were observed. For easing downstream processing, the sample name is also included on each row.
155
107 156
108 ----- 157 -----
109 158
110 @REFERENCES@ 159 @REFERENCES@
111 ]]> 160 ]]>