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comparison small_rna_maps.xml @ 12:d33263e6e812 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
author artbio
date Sat, 07 Apr 2018 06:14:50 -0400
parents a561a71bd7d7
children 458a88317c22
comparison
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11:a561a71bd7d7 12:d33263e6e812
1 <tool id="small_rna_maps" name="small_rna_maps" version="2.4.3"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="2.5.0">
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>
11 </requirements> 11 </requirements>
12 <stdio> 12 <stdio>
13 <exit_code range="1:" level="fatal" description="Tool exception" /> 13 <exit_code range="1:" level="fatal" description="Tool exception" />
14 </stdio> 14 </stdio>
15 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
16 #for $file in $inputs 16 #if $inputs_cond.normalize == "no":
17 samtools index '$file' && 17 #for $file in $inputs_cond.inputs
18 #end for 18 samtools index '$file';
19 python '$__tool_directory__'/small_rna_maps.py 19 #end for
20 --inputs 20 python '$__tool_directory__'/small_rna_maps.py
21 #for $file in $inputs 21 --inputs
22 '$file' 22 #for $file in $inputs_cond.inputs
23 #end for 23 '$file'
24 --sample_names 24 #end for
25 #for $sample in $inputs 25 --sample_names
26 '$sample.name' 26 #for $sample in $inputs_cond.inputs
27 #end for 27 '$sample.name'
28 #end for
29 #else if $inputs_cond.normalize == "yes":
30 #for $file in $inputs_cond.series
31 samtools index '$file.inputs';
32 #end for
33 python '$__tool_directory__'/small_rna_maps.py
34 --inputs
35 #for $file in $inputs_cond.series
36 '$file.inputs'
37 #end for
38 --sample_names
39 #for $sample in $inputs_cond.series
40 '$sample.inputs.name'
41 #end for
42 #end if
28 --minsize $minsize 43 --minsize $minsize
29 --maxsize $maxsize 44 --maxsize $maxsize
30 --cluster $cluster 45 --cluster $cluster
31 #if str($plots_options.plots_options_selector ) == "two_plot": 46 #if str($plots_options.plots_options_selector ) == "two_plot":
32 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}' 47 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
33 --outputs '$output_tab' '$extra_output_tab' && 48 --outputs '$output_tab' '$extra_output_tab';
34 #elif str($plots_options.plots_options_selector ) == "global": 49 #elif str($plots_options.plots_options_selector ) == "global":
35 --plot_methods 'Size' 50 --plot_methods 'Size'
36 --outputs '$output_tab' && 51 --outputs '$output_tab';
37 #else: 52 #else:
38 --plot_methods '${plots_options.first_plot}' 53 --plot_methods '${plots_options.first_plot}'
39 --outputs '$output_tab' && 54 --outputs '$output_tab' ;
40 #end if 55 #end if
41 Rscript '$__tool_directory__'/small_rna_maps.r 56 Rscript '$__tool_directory__'/small_rna_maps.r
42 --first_dataframe '$output_tab' 57 --first_dataframe '$output_tab'
43 --extra_dataframe '$extra_output_tab' 58 --extra_dataframe '$extra_output_tab'
44 --normalization '$normalization' 59 --normalization
60 #if $inputs_cond.normalize == "no":
61 ''
62 #else if $inputs_cond.normalize == "yes":
63 #set $norm = ""
64 #for $file in $inputs_cond.series
65 #set $norm += str($file.normalization)+' '
66 #end for
67 #set $norm = $norm[:-1]
68 '$norm'
69 #end if
70 #if $ylimits_cond.ylimits == "no":
71 --ymin '' --ymax ''
72 #else:
73 --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}'
74 #end if
45 #if str($plots_options.plots_options_selector ) == "two_plot": 75 #if str($plots_options.plots_options_selector ) == "two_plot":
46 --first_plot_method '${plots_options.first_plot}' 76 --first_plot_method '${plots_options.first_plot}'
47 --extra_plot_method '${plots_options.extra_plot}' 77 --extra_plot_method '${plots_options.extra_plot}'
48 #elif str($plots_options.plots_options_selector ) == "global": 78 #elif str($plots_options.plots_options_selector ) == "global":
49 --first_plot_method 'Size' 79 --first_plot_method 'Size'
54 --extra_plot_method '' 84 --extra_plot_method ''
55 #end if 85 #end if
56 --output_pdf '$output_pdf' 86 --output_pdf '$output_pdf'
57 ]]></command> 87 ]]></command>
58 <inputs> 88 <inputs>
59 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> 89 <conditional name="inputs_cond">
60 <param name="normalization" type="text" label="Enter size/normalization factors as a space-separated list. Leave blank for no normalization (default)" 90 <param name="normalize" type="boolean" label="Will there be normalization?" truevalue="yes" falsevalue="no" checked="false"/>
61 help="e.g. '1 0.75 1.23'. Values of the list map to the above selected files from bottom to top" /> 91 <when value="no">
92 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
93 </when>
94 <when value="yes">
95 <repeat name="series" title="Normalization factors" min="1">
96 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" />
97 <param name="normalization" type="float" label="Enter size/normalization factors."
98 help="e.g. '0.75' '1.23'" value="1.0"/>
99 </repeat>
100 </when>
101 </conditional>
62 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis" 102 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
63 value="0" help="default value: 0" /> 103 value="0" help="default value: 0" />
64 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis" 104 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
65 value="10000" help="default value: 10000" /> 105 value="10000" help="default value: 10000" />
66 <param name="cluster" type="integer" label="aggregation distance in nucleotides" 106 <param name="cluster" type="integer" label="Aggregation distance in nucleotides"
67 value="0" help="if not 0, sets the distance (in nt) below which data are clustered to a single median position" /> 107 value="0" help="If not 0, sets the distance (in nt) below which data are clustered to a single median position" />
68 <conditional name="plots_options"> 108 <conditional name="plots_options">
69 <param name="plots_options_selector" type="select" display="radio" label="Plot Options"> 109 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
70 <option value="one_plot">Just one plot per chromosome</option> 110 <option value="one_plot">Just one plot per chromosome</option>
71 <option value="two_plot" selected="True">Two plots per chromosome</option> 111 <option value="two_plot" selected="True">Two plots per chromosome</option>
72 <option value="global">Global read size distributions of aligned reads</option> 112 <option value="global">Global read size distributions of aligned reads</option>
73 </param> 113 </param>
74 <when value="two_plot"> 114 <when value="two_plot">
75 <param name="first_plot" type="select" display="radio" label="Select the type of the first plot"> 115 <param name="first_plot" type="select" display="radio" label="Select the type of the top plot">
76 <option value="Counts">Counts</option> 116 <option value="Counts">Counts</option>
77 <option value="Coverage">Coverage</option> 117 <option value="Coverage">Coverage</option>
78 <option value="Mean">Mean Sizes</option> 118 <option value="Mean">Mean Sizes</option>
79 <option value="Median">Median Sizes</option> 119 <option value="Median">Median Sizes</option>
80 <option value="Size">Size Distributions</option> 120 <option value="Size">Size Distributions</option>
81 </param> 121 </param>
82 <param name="extra_plot" type="select" display="radio" label="Select the type of the second plot"> 122 <param name="extra_plot" type="select" display="radio" label="Select the type of the bottom plot">
83 <option value="Counts">Counts</option> 123 <option value="Counts">Counts</option>
84 <option value="Coverage">Coverage</option> 124 <option value="Coverage">Coverage</option>
85 <option value="Mean">Mean Sizes</option> 125 <option value="Mean">Mean Sizes</option>
86 <option value="Median">Median Sizes</option> 126 <option value="Median">Median Sizes</option>
87 <option value="Size">Size Distributions</option> 127 <option value="Size">Size Distributions</option>
88 </param> 128 </param>
89 </when> 129 </when>
90 <when value="one_plot"> 130 <when value="one_plot">
91 <param name="first_plot" type="select" display="radio" label="select the type of the first plot"> 131 <param name="first_plot" type="select" display="radio" label="select the type of plot">
92 <option value="Counts">Counts</option> 132 <option value="Counts">Counts</option>
93 <option value="Coverage">Coverage</option> 133 <option value="Coverage">Coverage</option>
94 <option value="Mean">Mean Sizes</option> 134 <option value="Mean">Mean Sizes</option>
95 <option value="Median">Median Sizes</option> 135 <option value="Median">Median Sizes</option>
96 <option value="Size">Size Distributions</option> 136 <option value="Size">Size Distributions</option>
100 <param name="first_plot" type="hidden" value="Size"/> 140 <param name="first_plot" type="hidden" value="Size"/>
101 <param name="mergestrands" type="select" display="radio" label="Whether forward and reverse aligned reads should be merged or not in the histogram"> 141 <param name="mergestrands" type="select" display="radio" label="Whether forward and reverse aligned reads should be merged or not in the histogram">
102 <option value="nomerge">Do not merge</option> 142 <option value="nomerge">Do not merge</option>
103 <option value="merge">Merge forward and reverse reads</option> 143 <option value="merge">Merge forward and reverse reads</option>
104 </param> 144 </param>
145 </when>
146 </conditional>
147 <conditional name="ylimits_cond">
148 <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?"
149 help="This limit won't be applied to size distribution plots"/>
150 <when value="yes">
151 <param name="ymin" type="float" label="Enter minimum value" value="0.0" help="e.g. '-5.0'"/>
152 <param name="ymax" type="float" label="Enter maximum value" value="0.0" help="e.g. '5.0'"/>
153 </when>
154 <when value="no">
105 </when> 155 </when>
106 </conditional> 156 </conditional>
107 </inputs> 157 </inputs>
108 158
109 <outputs> 159 <outputs>
114 <data format="pdf" name="output_pdf" label="small RNA maps" /> 164 <data format="pdf" name="output_pdf" label="small RNA maps" />
115 </outputs> 165 </outputs>
116 166
117 <tests> 167 <tests>
118 <test> 168 <test>
169 <param name="inputs" value="input1.bam" ftype="bam"/>
170 <param name="minsize" value="0" />
171 <param name="maxsize" value="10000" />
172 <param name="cluster" value="0" />
173 <param name="ylimits" value="yes" />
174 <param name="ymin" value="-5" />
175 <param name="ymax" value="5" />
176 <param name="plots_options_selector" value="one_plot" />
177 <param name="first_plot" value="Counts" />
178 <output file="input1_counts_yminneg5_5.tab" name="output_tab" />
179 <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" />
180 </test>
181 <test>
182 <param name="inputs" value="input1.bam" ftype="bam"/>
183 <param name="minsize" value="0" />
184 <param name="maxsize" value="10000" />
185 <param name="cluster" value="5" />
186 <param name="plots_options_selector" value="one_plot" />
187 <param name="first_plot" value="Coverage" />
188 <output file="input1_coverage_cluster5.tab" name="output_tab" />
189 <output file="input1_cluster5_single_plot_coverage.pdf" name="output_pdf" />
190 </test>
191 <test>
192 <param name="inputs" value="input1.bam" ftype="bam"/>
193 <param name="minsize" value="20" />
194 <param name="maxsize" value="30" />
195 <param name="cluster" value="0" />
196 <param name="plots_options_selector" value="one_plot" />
197 <param name="first_plot" value="Size" />
198 <output file="input1_min20_max30_size.tab" name="output_tab" />
199 <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" />
200 </test>
201 <test>
202 <param name="inputs" value="input1.bam" ftype="bam"/>
203 <param name="minsize" value="0" />
204 <param name="maxsize" value="10000" />
205 <param name="cluster" value="0" />
206 <param name="plots_options_selector" value="one_plot" />
207 <param name="first_plot" value="Mean" />
208 <output file="input1_mean.tab" name="output_tab" />
209 <output file="input1__single_plot_mean.pdf" name="output_pdf" />
210 </test>
211 <test>
212 <param name="inputs" value="input1.bam" ftype="bam"/>
213 <param name="minsize" value="0" />
214 <param name="maxsize" value="10000" />
215 <param name="cluster" value="0" />
216 <param name="plots_options_selector" value="one_plot" />
217 <param name="first_plot" value="Median" />
218 <output file="input1_median.tab" name="output_tab" />
219 <output file="input1_single_plot_median.pdf" name="output_pdf" />
220 </test>
221 <test>
222 <param name="normalize" value="yes" />
223 <repeat name="series">
224 <param name="inputs" value="input1.bam" ftype="bam" />
225 <param name="normalization" value="1.0" />
226 </repeat>
227 <repeat name="series">
228 <param name="inputs" value="input2.bam" ftype="bam" />
229 <param name="normalization" value="2.0" />
230 </repeat>
231 <param name="minsize" value="0" />
232 <param name="maxsize" value="10000" />
233 <param name="cluster" value="0" />
234 <param name="plots_options_selector" value="one_plot" />
235 <param name="first_plot" value="Counts" />
236 <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" />
237 <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
238 </test>
239 <test>
119 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 240 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
120 <param name="minsize" value="0" /> 241 <param name="minsize" value="0" />
121 <param name="cluster" value="5" /> 242 <param name="maxsize" value="10000" />
122 <param name="maxsize" value="10000" /> 243 <param name="cluster" value="0" />
123 <param name="plots_options_selector" value="one_plot" /> 244 <param name="ylimits" value="yes" />
124 <param name="normalization" value="1 1" /> 245 <param name="ymin" value="-5" />
246 <param name="ymax" value="5" />
247 <param name="plots_options_selector" value="two_plot" />
125 <param name="first_plot" value="Counts" /> 248 <param name="first_plot" value="Counts" />
126 <output file="count_cluster_5.tab" name="output_tab" /> 249 <param name="extra_plot" value="Size" />
127 <output file="count_cluster_5.pdf" name="output_pdf" /> 250 <output file="input1_input2_counts.tab" name="output_tab" />
251 <output file="input1_input2_size.tab" name="extra_output_tab" />
252 <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" />
253 </test>
254 <test>
255 <param name="inputs" value="input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam" ftype="bam"/>
256 <param name="minsize" value="0" />
257 <param name="maxsize" value="10000" />
258 <param name="cluster" value="0" />
259 <param name="plots_options_selector" value="one_plot" />
260 <param name="first_plot" value="Coverage" />
261 <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
262 <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
128 </test> 263 </test>
129 <test> 264 <test>
130 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 265 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
131 <param name="minsize" value="0" /> 266 <param name="minsize" value="0" />
132 <param name="maxsize" value="10000" /> 267 <param name="maxsize" value="10000" />
148 <param name="first_plot" value="Size" /> 283 <param name="first_plot" value="Size" />
149 <param name="normalization" value="1 1" /> 284 <param name="normalization" value="1 1" />
150 <output file="size.tab" name="output_tab" /> 285 <output file="size.tab" name="output_tab" />
151 <output file="global_merge.pdf" name="output_pdf" /> 286 <output file="global_merge.pdf" name="output_pdf" />
152 </test> 287 </test>
153 <test>
154 <param name="inputs" value="input1.bam" ftype="bam"/>
155 <param name="minsize" value="20" />
156 <param name="maxsize" value="30" />
157 <param name="cluster" value="0" />
158 <param name="plots_options_selector" value="global" />
159 <param name="mergestrands" value="merge" />
160 <param name="first_plot" value="Size" />
161 <param name="normalization" value="1 1" />
162 <output file="size20-30.tab" name="output_tab" />
163 <output file="global_merge_20-30.pdf" name="output_pdf" />
164 </test>
165 <test>
166 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
167 <param name="minsize" value="0" />
168 <param name="maxsize" value="10000" />
169 <param name="cluster" value="0" />
170 <param name="plots_options_selector" value="two_plot" />
171 <param name="first_plot" value="Counts" />
172 <param name="extra_plot" value="Mean" />
173 <param name="normalization" value="1 1" />
174 <output file="count.tab" name="output_tab" />
175 <output file="mean.tab" name="extra_output_tab" />
176 <output file="count-mean.pdf" name="output_pdf" />
177 </test>
178 <test>
179 <param name="inputs" value="input2.bam,input1.bam" ftype="bam"/>
180 <param name="minsize" value="20" />
181 <param name="maxsize" value="30" />
182 <param name="cluster" value="0" />
183 <param name="plots_options_selector" value="two_plot" />
184 <param name="first_plot" value="Counts" />
185 <param name="extra_plot" value="Mean" />
186 <param name="normalization" value="1 1" />
187 <output file="count20-30.tab" name="output_tab" />
188 <output file="mean20-30.tab" name="extra_output_tab" />
189 <output file="count-mean-20-30.pdf" name="output_pdf" />
190 </test>
191 <test>
192 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/>
193 <param name="minsize" value="0" />
194 <param name="maxsize" value="10000" />
195 <param name="cluster" value="0" />
196 <param name="plots_options_selector" value="two_plot" />
197 <param name="first_plot" value="Counts" />
198 <param name="extra_plot" value="Mean" />
199 <param name="normalization" value="1 1" />
200 <output file="doubled_count.tab" name="output_tab" />
201 <output file="doubled_mean.tab" name="extra_output_tab" />
202 <output file="doubled_count-mean.pdf" name="output_pdf" />
203 </test>
204 <test>
205 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
206 <param name="minsize" value="0" />
207 <param name="maxsize" value="10000" />
208 <param name="cluster" value="0" />
209 <param name="plots_options_selector" value="two_plot" />
210 <param name="first_plot" value="Counts" />
211 <param name="extra_plot" value="Median" />
212 <param name="normalization" value="1 1" />
213 <output file="count.tab" name="output_tab" />
214 <output file="median.tab" name="extra_output_tab" />
215 <output file="count-median.pdf" name="output_pdf" />
216 </test>
217 <test>
218 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
219 <param name="minsize" value="0" />
220 <param name="maxsize" value="10000" />
221 <param name="cluster" value="0" />
222 <param name="plots_options_selector" value="two_plot" />
223 <param name="first_plot" value="Counts" />
224 <param name="extra_plot" value="Coverage" />
225 <param name="normalization" value="1 1" />
226 <output file="count.tab" name="output_tab" />
227 <output file="coverage.tab" name="extra_output_tab" />
228 <output file="count-coverage.pdf" name="output_pdf" />
229 </test>
230 <test>
231 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
232 <param name="minsize" value="0" />
233 <param name="maxsize" value="10000" />
234 <param name="cluster" value="0" />
235 <param name="plots_options_selector" value="two_plot" />
236 <param name="first_plot" value="Counts" />
237 <param name="extra_plot" value="Size" />
238 <param name="normalization" value="1 1" />
239 <output file="count.tab" name="output_tab" />
240 <output file="size.tab" name="extra_output_tab" />
241 <output file="count-size.pdf" name="output_pdf" />
242 </test>
243 <test>
244 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
245 <param name="minsize" value="0" />
246 <param name="maxsize" value="10000" />
247 <param name="cluster" value="0" />
248 <param name="plots_options_selector" value="two_plot" />
249 <param name="first_plot" value="Size" />
250 <param name="extra_plot" value="Counts" />
251 <param name="normalization" value="1 1" />
252 <output file="size.tab" name="output_tab" />
253 <output file="count.tab" name="extra_output_tab" />
254 <output file="size-count.pdf" name="output_pdf" />
255 </test>
256 <test>
257 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
258 <param name="minsize" value="0" />
259 <param name="maxsize" value="10000" />
260 <param name="cluster" value="0" />
261 <param name="plots_options_selector" value="two_plot" />
262 <param name="first_plot" value="Size" />
263 <param name="extra_plot" value="Counts" />
264 <param name="normalization" value="1 0.75" />
265 <output file="size.tab" name="output_tab" />
266 <output file="count.tab" name="extra_output_tab" />
267 <output file="size-count_normed.pdf" name="output_pdf" />
268 </test>
269 <test>
270 <param name="inputs" value="input_single_chr.bam" ftype="bam"/>
271 <param name="minsize" value="0" />
272 <param name="maxsize" value="10000" />
273 <param name="cluster" value="0" />
274 <param name="plots_options_selector" value="two_plot" />
275 <param name="first_plot" value="Counts" />
276 <param name="extra_plot" value="Coverage" />
277 <param name="normalization" value="1 1" />
278 <output file="count_1_chr.tab" name="output_tab" />
279 <output file="coverage_1_chr.tab" name="extra_output_tab" />
280 <output file="counts_coverage_1.pdf" name="output_pdf" />
281 </test>
282 <test>
283 <param name="inputs" value="input_5_chr.bam" ftype="bam"/>
284 <param name="minsize" value="0" />
285 <param name="maxsize" value="10000" />
286 <param name="cluster" value="0" />
287 <param name="plots_options_selector" value="two_plot" />
288 <param name="first_plot" value="Counts" />
289 <param name="extra_plot" value="Coverage" />
290 <param name="normalization" value="1 1" />
291 <output file="count_5_chr.tab" name="output_tab" />
292 <output file="coverage_5_chr.tab" name="extra_output_tab" />
293 <output file="counts_coverage_5.pdf" name="output_pdf" />
294 </test>
295 <test>
296 <param name="inputs" value="input_single_chr.bam" ftype="bam"/>
297 <param name="minsize" value="0" />
298 <param name="maxsize" value="10000" />
299 <param name="cluster" value="0" />
300 <param name="plots_options_selector" value="one_plot" />
301 <param name="first_plot" value="Counts" />
302 <param name="normalization" value="1 1" />
303 <output file="count_1_chr.tab" name="output_tab" />
304 <output file="count_1.pdf" name="output_pdf" />
305 </test>
306 <test>
307 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
308 <param name="minsize" value="0" />
309 <param name="cluster" value="0" />
310 <param name="maxsize" value="10000" />
311 <param name="plots_options_selector" value="one_plot" />
312 <param name="normalization" value="1 1" />
313 <param name="first_plot" value="Counts" />
314 <output file="count.tab" name="output_tab" />
315 <output file="count.pdf" name="output_pdf" />
316 </test>
317 <test>
318 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
319 <param name="minsize" value="0" />
320 <param name="maxsize" value="10000" />
321 <param name="cluster" value="0" />
322 <param name="plots_options_selector" value="one_plot" />
323 <param name="first_plot" value="Size" />
324 <param name="normalization" value="1 1" />
325 <output file="size.tab" name="output_tab" />
326 <output file="size.pdf" name="output_pdf" />
327 </test>
328 <test>
329 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
330 <param name="minsize" value="0" />
331 <param name="maxsize" value="10000" />
332 <param name="cluster" value="0" />
333 <param name="plots_options_selector" value="one_plot" />
334 <param name="first_plot" value="Coverage" />
335 <param name="normalization" value="1 1" />
336 <output file="coverage.tab" name="output_tab" />
337 <output file="coverage.pdf" name="output_pdf" />
338 </test>
339 <test>
340 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
341 <param name="minsize" value="0" />
342 <param name="maxsize" value="10000" />
343 <param name="cluster" value="0" />
344 <param name="plots_options_selector" value="one_plot" />
345 <param name="first_plot" value="Coverage" />
346 <param name="normalization" value="1 0.2" />
347 <output file="coverage.tab" name="output_tab" />
348 <output file="coverage_normed.pdf" name="output_pdf" />
349 </test>
350 </tests> 288 </tests>
351
352
353 <help> 289 <help>
354 290
355 **What it does** 291 **What it does**
356 292
357 Plots maps of (1) read counts, (2) mean sizes, (3) median sizes, (4) coverage depth or (5) 293 Plots mapping statistics of an alignment along the reference chromosomes :
358 size read distribution along chromosome references. 294
359 295 - counts
360 Mean sizes and median sizes are the mean and the median sizes, respectively, of all reads 296 - mean sizes
361 whose 5' end map to a given coordinate in a chromosome reference. 297 - median sizes
298 - coverage depth
299 - size distribution
300
301 Read counts, mean sizes and median sizes are computed by counting the number of 5' end of reads
302 in each position of a chromosome reference.
362 Coverage depths are computed from the input bam alignment files using the python pysam module. 303 Coverage depths are computed from the input bam alignment files using the python pysam module.
363 304
364 The variables mentioned above (1-5) can be plotted either separately or in all possible 305 The metrics mentioned above can be plotted either separately:
365 pairwise combinations. 306
366 307 .. image:: one_plot.png
367 For comparison purpose, values from bam alignment files can be normalized by a size factor 308
368 before plotting. If the normalization field is leaved blank, default normalization of 1 309 Or in all possible pairwise combinations:
369 is assumed. 310
311 .. image:: two_plot.png
312
313 For comparison purposes, values from bam alignment files can be normalized by a size factor
314 before plotting.
370 315
371 **Inputs** 316 **Inputs**
372 317
373 bam alignment files that must be 318 bam alignment files that must be
374 319
375 - single-read 320 - single-read
376 - sorted 321 - sorted
377 - mapping to the same reference 322 - mapped to the same reference
378
379 Optionally, a space-separated list of normalization/size factors may be added before plotting.
380 This list maps to the selected bam alignments from bottom to top.
381 323
382 **Output** 324 **Output**
383 325
384 A pdf file generated by the R package lattice 326 A pdf file generated by the R package lattice and one or two dataframes used to plot the data.
385
386 One or two dataframes used to plot data
387 327
388 </help> 328 </help>
389 329
390 <citations> 330 <citations>
391 <citation type="doi">10.1093/bioinformatics/btp352</citation> 331 <citation type="doi">10.1093/bioinformatics/btp352</citation>