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comparison computeGCBias.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_computeGCBias" name="computeGCBias" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_computeGCBias" name="computeGCBias" version="@WRAPPER_VERSION@.0">
2 <description>to see whether your samples should be normalized for GC bias</description> 2 <description>to see whether your samples should be normalized for GC bias</description>
3 <expand macro="requirements" />
4 <expand macro="stdio" />
5 <macros> 3 <macros>
6 <token name="@BINARY@">computeGCBias</token> 4 <token name="@BINARY@">computeGCBias</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 ln -s $bamInput local_bamInput.bam; 10 ln -s $bamInput local_bamInput.bam;
11 ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai; 11 ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;
12 12
13 computeGCBias 13 computeGCBias
14 @THREADS@ 14 @THREADS@
28 #if str($region).strip() != '': 28 #if str($region).strip() != '':
29 --region '$region' 29 --region '$region'
30 #end if 30 #end if
31 31
32 #if $advancedOpt.showAdvancedOpt == "yes": 32 #if $advancedOpt.showAdvancedOpt == "yes":
33
34 --sampleSize '$advancedOpt.sampleSize' 33 --sampleSize '$advancedOpt.sampleSize'
35 --regionSize '$advancedOpt.regionSize' 34 --regionSize '$advancedOpt.regionSize'
36 35
37 #if $advancedOpt.filterOut: 36 #if $advancedOpt.filterOut:
38 --filterOut $advancedOpt.filterOut 37 --filterOut $advancedOpt.filterOut
45 44
46 #if str($image_format) != 'none': 45 #if str($image_format) != 'none':
47 --biasPlot $outImageName 46 --biasPlot $outImageName
48 --plotFileFormat $image_format 47 --plotFileFormat $image_format
49 #end if 48 #end if
49 ]]>
50 </command> 50 </command>
51 <inputs> 51 <inputs>
52 <param name="bamInput" format="bam" type="data" label="BAM file" 52 <param name="bamInput" format="bam" type="data" label="BAM file"
53 help="The BAM file must be sorted."/> 53 help="The BAM file must be sorted."/>
54 54
55 <expand macro="reference_genome_source" /> 55 <expand macro="reference_genome_source" />
56 <expand macro="effectiveGenomeSize" /> 56 <expand macro="effectiveGenomeSize" />
57 57 <expand macro="fragmentLength" />
58 <param name="fragmentLength" type="integer" value="300" min="1"
59 label="Fragment length used for the sequencing"
60 help ="If paired-end reads are used, the fragment length is computed from the BAM file."/>
61
62 <expand macro="region_limit_operation" /> 58 <expand macro="region_limit_operation" />
63 59
64 <conditional name="advancedOpt"> 60 <conditional name="advancedOpt">
65 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 61 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
66 <option value="no" selected="true">no</option> 62 <option value="no" selected="true">no</option>
67 <option value="yes">yes</option> 63 <option value="yes">yes</option>
68 </param> 64 </param>
69 <when value="no" /> 65 <when value="no" />
70 <when value="yes"> 66 <when value="yes">
71 <param name="sampleSize" type="integer" value="50000000" min="1" 67 <param name="sampleSize" type="integer" value="50000000" min="1"
72 label="Number of sampling points to be considered" /> 68 label="Number of sampling points to be considered" help="(--sampleSize)" />
73
74 <param name="regionSize" type="integer" value="300" min="1" 69 <param name="regionSize" type="integer" value="300" min="1"
75 label="Region size" 70 label="Region size"
76 help ="To plot the reads per GC over a region, the size of the region is required (see below for more details of the mthod). By default, the bin size is set to 300 bp, which is close to the standard fragment size many sequencing applications. However, if the depth of sequencing is low, a larger bin size will be required, otherwise many bins will not overlap with any read."/> 71 help ="To plot the reads per GC over a region, the size of the region is
77 72 required (see below for more details of the mthod). By default, the bin size
73 is set to 300 bp, which is close to the standard fragment size many sequencing
74 applications. However, if the depth of sequencing is low, a larger bin size will
75 be required, otherwise many bins will not overlap with any read. (--regionSize)"/>
78 <param name="filterOut" type="data" format="bed" optional="true" 76 <param name="filterOut" type="data" format="bed" optional="true"
79 label="BED file containing genomic regions to be excluded from the estimation of the correction" 77 label="BED file containing genomic regions to be excluded from the estimation of the correction"
80 help="Such regions usually contain repetitive regions and peaks that if included will bias the correction. It is recommended to filter out known repetitive regions if multi-reads (reads that map to more than one genomic position) were excluded. In the case of ChIP-seq data, it is recommended to first use a peak caller to identify and filter out the identified peaks." /> 78 help="Such regions usually contain repetitive regions and peaks that if included will
79 bias the correction. It is recommended to filter out known repetitive regions if multi-reads
80 (reads that map to more than one genomic position) were excluded. In the case of ChIP-seq data,
81 it is recommended to first use a peak caller to identify and filter out the identified peaks. (--filterOut)" />
81 <param name="extraSampling" type="data" format="bed" optional="true" 82 <param name="extraSampling" type="data" format="bed" optional="true"
82 label="BED file containing genomic regions for which extra sampling is required because they are underrepresented in the genome" 83 label="BED file containing genomic regions for which extra sampling is required because they are underrepresented in the genome"
83 help="" /> 84 help="(--extraSampling)" />
84 </when> 85 </when>
85 </conditional> 86 </conditional>
86 <param name="image_format" type="select" label="GC bias plot" help="If given, a diagnostic image summarizing the GC bias found on the sample will be created."> 87 <param name="image_format" type="select"
88 label="GC bias plot"
89 help="If given, a diagnostic image summarizing the GC bias found on the sample will be created. (--plotFileFormat)">
87 <option value="none">No image</option> 90 <option value="none">No image</option>
88 <option value="png" selected="true">Image in png format</option> 91 <option value="png" selected="true">Image in png format</option>
89 <option value="pdf">Image in pdf format</option> 92 <option value="pdf">Image in pdf format</option>
90 <option value="svg">Image in svg format</option> 93 <option value="svg">Image in svg format</option>
91 <option value="eps">Image in eps format</option> 94 <option value="eps">Image in eps format</option>
92 <option value="emf">Image in emf format</option> 95 <option value="emf">Image in emf format</option>
93 </param> 96 </param>
94 </inputs> 97 </inputs>
95 <outputs> 98 <outputs>
96 <data format="tabular" name="outFileName" /> 99 <data name="outFileName" format="tabular" />
97 <data format="png" name="outImageName" label="${tool.name} GC-bias Plot"> 100 <data name="outImageName" format="png" label="${tool.name} GC-bias Plot">
98 <filter> 101 <filter>
99 (( 102 ((
100 image_format != 'none' 103 image_format != 'none'
101 )) 104 ))
102 </filter> 105 </filter>
106 <when input="image_format" value="eps" format="eps" /> 109 <when input="image_format" value="eps" format="eps" />
107 <when input="image_format" value="emf" format="emf" /> 110 <when input="image_format" value="emf" format="emf" />
108 </change_format> 111 </change_format>
109 </data> 112 </data>
110 </outputs> 113 </outputs>
114 <tests>
115 <test>
116 <param name="bamInput" value="paired_chr2L.bam" ftype="bam" />
117 <param name="image_format" value="png" />
118 <param name="showAdvancedOpt" value="yes" />
119 <param name="regionSize" value="1" />
120 <param name="fragmentLength" value="100" />
121 <param name="ref_source" value="history" />
122 <param name="input1" value="sequence.2bit" />
123 <param name="sampleSize" value="10" />
124 <param name="effectiveGenomeSize_opt" value="specific" />
125 <param name="effectiveGenomeSize" value="23011544" />
126 <param name="region" value="chr2L" />
127 <param name="image_format" value="none" />
128 <output name="outFileName" file="computeGCBias_result1.tabular" ftype="tabular" />
129 </test>
130 </tests>
111 <help> 131 <help>
112 132 <![CDATA[
113 **What it does** 133 **What it does**
114 134
115 This tool computes the GC bias using the method proposed by Benjamini and Speed (2012) Nucleic Acids Res. (see below for more explanations) 135 This tool computes the GC bias using the method proposed by Benjamini and Speed (2012) Nucleic Acids Res. (see below for more explanations)
116 The output is used to plot the bias and can also be used later on to correct the bias with the tool correctGCbias. 136 The output is used to plot the bias and can also be used later on to correct the bias with the tool correctGCbias.
117 There are two plots produced by the tool: a boxplot showing the absolute read numbers per genomic-GC bin and an x-y plot 137 There are two plots produced by the tool: a boxplot showing the absolute read numbers per genomic-GC bin and an x-y plot
148 168
149 169
150 ----- 170 -----
151 171
152 @REFERENCES@ 172 @REFERENCES@
153 173 ]]>
154 </help> 174 </help>
155 <expand macro="citations" /> 175 <expand macro="citations" />
156 </tool> 176 </tool>