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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
author artbio
date Mon, 09 Oct 2017 11:07:09 -0400
parents 12c14642e6ac
children a96e6a7df2b7
comparison
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5:12c14642e6ac 6:a3be3601bcb3
1 <tool id="small_rna_maps" name="small_rna_maps" version="2.0.0"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="2.1.0">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> 4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> 5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> 6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
31 --outputs '$output_tab' && 31 --outputs '$output_tab' &&
32 #end if 32 #end if
33 Rscript '$__tool_directory__'/small_rna_maps.r 33 Rscript '$__tool_directory__'/small_rna_maps.r
34 --first_dataframe '$output_tab' 34 --first_dataframe '$output_tab'
35 --extra_dataframe '$extra_output_tab' 35 --extra_dataframe '$extra_output_tab'
36 --normalization '$normalization'
36 #if str($plots_options.plots_options_selector ) == "two_plot": 37 #if str($plots_options.plots_options_selector ) == "two_plot":
37 --first_plot_method '${plots_options.first_plot}' 38 --first_plot_method '${plots_options.first_plot}'
38 --extra_plot_method '${plots_options.extra_plot}' 39 --extra_plot_method '${plots_options.extra_plot}'
39 #else: 40 #else:
40 --first_plot_method '${plots_options.first_plot}' 41 --first_plot_method '${plots_options.first_plot}'
42 #end if 43 #end if
43 --output_pdf '$output_pdf' 44 --output_pdf '$output_pdf'
44 ]]></command> 45 ]]></command>
45 <inputs> 46 <inputs>
46 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> 47 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
48 <param name="normalization" type="text" label="Enter size/normalization factors as a space-separated list. Leave blank for no normalization (default)"
49 help="e.g. '1 0.75 1.23'. Values of the list map to the above selected files from bottom to top" />
47 <conditional name="plots_options"> 50 <conditional name="plots_options">
48 <param name="plots_options_selector" type="select" label="Number of plots per chromosome"> 51 <param name="plots_options_selector" type="select" label="Number of plots per chromosome">
49 <option value="one_plot">Just one plot per chromosome</option> 52 <option value="one_plot">Just one plot per chromosome</option>
50 <option value="two_plot" selected="True">Two plots per chromosome</option> 53 <option value="two_plot" selected="True">Two plots per chromosome</option>
51 </param> 54 </param>
52 <when value="two_plot"> 55 <when value="two_plot">
53 <param name="first_plot" type="select" label="select the type of the first plot"> 56 <param name="first_plot" type="select" label="Select the type of the first plot">
54 <option value="Counts">Counts</option> 57 <option value="Counts">Counts</option>
55 <option value="Coverage">Coverage</option> 58 <option value="Coverage">Coverage</option>
56 <option value="Mean">Mean Sizes</option> 59 <option value="Mean">Mean Sizes</option>
57 <option value="Median">Median Sizes</option> 60 <option value="Median">Median Sizes</option>
58 <option value="Size">Size Distributions</option> 61 <option value="Size">Size Distributions</option>
59 </param> 62 </param>
60 <param name="extra_plot" type="select" label="select the type of the second plot"> 63 <param name="extra_plot" type="select" label="Select the type of the second plot">
61 <option value="Counts">Counts</option> 64 <option value="Counts">Counts</option>
62 <option value="Coverage">Coverage</option> 65 <option value="Coverage">Coverage</option>
63 <option value="Mean">Mean Sizes</option> 66 <option value="Mean">Mean Sizes</option>
64 <option value="Median">Median Sizes</option> 67 <option value="Median">Median Sizes</option>
65 <option value="Size">Size Distributions</option> 68 <option value="Size">Size Distributions</option>
90 <test> 93 <test>
91 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 94 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
92 <param name="plots_options_selector" value="two_plot" /> 95 <param name="plots_options_selector" value="two_plot" />
93 <param name="first_plot" value="Counts" /> 96 <param name="first_plot" value="Counts" />
94 <param name="extra_plot" value="Mean" /> 97 <param name="extra_plot" value="Mean" />
98 <param name="normalization" value="1 1" />
95 <output file="count.tab" name="output_tab" /> 99 <output file="count.tab" name="output_tab" />
96 <output file="mean.tab" name="extra_output_tab" /> 100 <output file="mean.tab" name="extra_output_tab" />
97 <output file="count-mean.pdf" name="output_pdf" /> 101 <output file="count-mean.pdf" name="output_pdf" />
98 </test> 102 </test>
99 <test> 103 <test>
100 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/> 104 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/>
101 <param name="plots_options_selector" value="two_plot" /> 105 <param name="plots_options_selector" value="two_plot" />
102 <param name="first_plot" value="Counts" /> 106 <param name="first_plot" value="Counts" />
103 <param name="extra_plot" value="Mean" /> 107 <param name="extra_plot" value="Mean" />
108 <param name="normalization" value="1 1" />
104 <output file="doubled_count.tab" name="output_tab" /> 109 <output file="doubled_count.tab" name="output_tab" />
105 <output file="doubled_mean.tab" name="extra_output_tab" /> 110 <output file="doubled_mean.tab" name="extra_output_tab" />
106 <output file="doubled_count-mean.pdf" name="output_pdf" /> 111 <output file="doubled_count-mean.pdf" name="output_pdf" />
107 </test> 112 </test>
108 <test> 113 <test>
109 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 114 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
110 <param name="plots_options_selector" value="two_plot" /> 115 <param name="plots_options_selector" value="two_plot" />
111 <param name="first_plot" value="Counts" /> 116 <param name="first_plot" value="Counts" />
112 <param name="extra_plot" value="Median" /> 117 <param name="extra_plot" value="Median" />
118 <param name="normalization" value="1 1" />
113 <output file="count.tab" name="output_tab" /> 119 <output file="count.tab" name="output_tab" />
114 <output file="median.tab" name="extra_output_tab" /> 120 <output file="median.tab" name="extra_output_tab" />
115 <output file="count-median.pdf" name="output_pdf" /> 121 <output file="count-median.pdf" name="output_pdf" />
116 </test> 122 </test>
117 <test> 123 <test>
118 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 124 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
119 <param name="plots_options_selector" value="two_plot" /> 125 <param name="plots_options_selector" value="two_plot" />
120 <param name="first_plot" value="Counts" /> 126 <param name="first_plot" value="Counts" />
121 <param name="extra_plot" value="Coverage" /> 127 <param name="extra_plot" value="Coverage" />
128 <param name="normalization" value="1 1" />
122 <output file="count.tab" name="output_tab" /> 129 <output file="count.tab" name="output_tab" />
123 <output file="coverage.tab" name="extra_output_tab" /> 130 <output file="coverage.tab" name="extra_output_tab" />
124 <output file="count-coverage.pdf" name="output_pdf" /> 131 <output file="count-coverage.pdf" name="output_pdf" />
125 </test> 132 </test>
126 <test> 133 <test>
127 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 134 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
128 <param name="plots_options_selector" value="two_plot" /> 135 <param name="plots_options_selector" value="two_plot" />
129 <param name="first_plot" value="Counts" /> 136 <param name="first_plot" value="Counts" />
130 <param name="extra_plot" value="Size" /> 137 <param name="extra_plot" value="Size" />
138 <param name="normalization" value="1 1" />
131 <output file="count.tab" name="output_tab" /> 139 <output file="count.tab" name="output_tab" />
132 <output file="size.tab" name="extra_output_tab" /> 140 <output file="size.tab" name="extra_output_tab" />
133 <output file="count-size.pdf" name="output_pdf" /> 141 <output file="count-size.pdf" name="output_pdf" />
134 </test> 142 </test>
135 <test> 143 <test>
136 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 144 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
137 <param name="plots_options_selector" value="two_plot" /> 145 <param name="plots_options_selector" value="two_plot" />
138 <param name="first_plot" value="Size" /> 146 <param name="first_plot" value="Size" />
139 <param name="extra_plot" value="Counts" /> 147 <param name="extra_plot" value="Counts" />
148 <param name="normalization" value="1 1" />
140 <output file="size.tab" name="output_tab" /> 149 <output file="size.tab" name="output_tab" />
141 <output file="count.tab" name="extra_output_tab" /> 150 <output file="count.tab" name="extra_output_tab" />
142 <output file="size-count.pdf" name="output_pdf" /> 151 <output file="size-count.pdf" name="output_pdf" />
143 </test> 152 </test>
144 <test> 153 <test>
145 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 154 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
146 <param name="plots_options_selector" value="one_plot" /> 155 <param name="plots_options_selector" value="two_plot" />
156 <param name="first_plot" value="Size" />
157 <param name="extra_plot" value="Counts" />
158 <param name="normalization" value="1 0.75" />
159 <output file="size.tab" name="output_tab" />
160 <output file="count.tab" name="extra_output_tab" />
161 <output file="size-count_normed.pdf" name="output_pdf" />
162 </test>
163 <test>
164 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
165 <param name="plots_options_selector" value="one_plot" />
166 <param name="normalization" value="1 1" />
147 <param name="first_plot" value="Counts" /> 167 <param name="first_plot" value="Counts" />
148 <output file="count.tab" name="output_tab" /> 168 <output file="count.tab" name="output_tab" />
149 <output file="count.pdf" name="output_pdf" /> 169 <output file="count.pdf" name="output_pdf" />
150 </test> 170 </test>
151 <test> 171 <test>
152 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 172 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
153 <param name="plots_options_selector" value="one_plot" /> 173 <param name="plots_options_selector" value="one_plot" />
154 <param name="first_plot" value="Size" /> 174 <param name="first_plot" value="Size" />
175 <param name="normalization" value="1 1" />
155 <output file="size.tab" name="output_tab" /> 176 <output file="size.tab" name="output_tab" />
156 <output file="size.pdf" name="output_pdf" /> 177 <output file="size.pdf" name="output_pdf" />
157 </test> 178 </test>
158 <test> 179 <test>
159 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 180 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
160 <param name="plots_options_selector" value="one_plot" /> 181 <param name="plots_options_selector" value="one_plot" />
161 <param name="first_plot" value="Coverage" /> 182 <param name="first_plot" value="Coverage" />
183 <param name="normalization" value="1 1" />
162 <output file="coverage.tab" name="output_tab" /> 184 <output file="coverage.tab" name="output_tab" />
163 <output file="coverage.pdf" name="output_pdf" /> 185 <output file="coverage.pdf" name="output_pdf" />
164 </test> 186 </test>
187 <test>
188 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
189 <param name="plots_options_selector" value="one_plot" />
190 <param name="first_plot" value="Coverage" />
191 <param name="normalization" value="1 0.2" />
192 <output file="coverage.tab" name="output_tab" />
193 <output file="coverage_normed.pdf" name="output_pdf" />
194 </test>
165 </tests> 195 </tests>
166 196
167 197
168 <help> 198 <help>
169 199
170 **What it does** 200 **What it does**
171 201
172 Generate read count maps from alignment BAM files, using pysam and lattice. 202 Plots maps of (1) read counts, (2) mean sizes, (3) median sizes, (4) coverage depth or (5)
173 203 size read distribution along chromosome references.
174 In addition to the read counts (lower graphs), median size, mean size and coverage depth of reads(lower graphs) mapping at a given position are plotted. 204
205 Mean sizes and median sizes are the mean and the median sizes, respectively, of all reads
206 whose 5' end map to a given coordinate in a chromosome reference.
207 Coverage depths are computed from the input bam alignment files using the python pysam module.
208
209 The variables mentioned above (1-5) can be plotted either separately or in all possible
210 pairwise combinations.
211
212 For comparison purpose, values from bam alignment files can be normalized by a size factor
213 before plotting. If the normalization field is leaved blank, default normalization of 1
214 is assumed.
175 215
176 **Inputs** 216 **Inputs**
177 217
178 bam alignment files that must be 218 bam alignment files that must be
179 219
180 - single-read 220 - single-read
181 - sorted 221 - sorted
182 - mapping to the same reference 222 - mapping to the same reference
223
224 Optionally, a space-separated list of normalization/size factors may be added before plotting.
225 This list maps to the selected bam alignments from bottom to top.
183 226
184 **Output** 227 **Output**
185 228
186 A pdf file generated by the R package lattice 229 A pdf file generated by the R package lattice
187 230