Mercurial > repos > swebb > pycrac
comparison pyCRAC/pyBinCollector.xml @ 0:19b20927172d draft
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author | swebb |
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date | Tue, 18 Jun 2013 09:11:00 -0400 |
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1 <tool id ="pyBinCollector" name="pyBinCollector"> | |
2 <requirements> | |
3 <requirement type="package">pyCRAC</requirement> | |
4 </requirements> | |
5 <command interpreter="perl"> | |
6 pyBinCollector.pl | |
7 -f $input | |
8 --gtf $addGTF.gtf | |
9 #if $addGTF.gtfFile == "default" and $addGTF.annotate.annotations == "auto": | |
10 --annotation $addGTF.annotate.scan.annotation | |
11 #else: | |
12 --annotation $addGTF.annotate.annotation | |
13 #end if# | |
14 #if $addOpt.options == "edit": | |
15 --options | |
16 --range $addOpt.range | |
17 --min_length $addOpt.min_length | |
18 --max_length $addOpt.max_length | |
19 --numberofbins $addOpt.numberofbins | |
20 -s $addOpt.sequence | |
21 #if $addOpt.limitBins.binselect == "yes": | |
22 --bins1 $addOpt.limitBins.bs_first | |
23 --bins2 $addOpt.limitBins.bs_last | |
24 #end if# | |
25 $addOpt.ignore | |
26 $addOpt.oall.outputall | |
27 #end if# | |
28 -o "$input.name" | |
29 #if $addOpt.options == "edit" and $addOpt.oall.outputall == "--outputall": | |
30 --id $sd.id | |
31 --sd $sd | |
32 --ssub $ssub | |
33 --sdel $sdel | |
34 --asd $asd | |
35 --assub $assub | |
36 --asdel $asdel | |
37 #else: | |
38 --out $out | |
39 --id $out.id | |
40 #end if# | |
41 </command> | |
42 <version_command>/usr/local/bin/pyBinCollector.py --version</version_command> | |
43 <inputs> | |
44 <param format="gtf" name="input" type="data" label="Input File -f" help="pyReadCounters or pyMotif gtf output files" /> | |
45 | |
46 <conditional name="addGTF"> | |
47 <param name="gtfFile" type="select" label="Choose GTF File from"> | |
48 <option value="default" selected="true">Defaults</option> | |
49 <option value="other">History</option> | |
50 </param> | |
51 <when value="default"> | |
52 <param name="gtf" type="select" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"> | |
53 <options from_data_table="pycrac_gtf"/> | |
54 </param> | |
55 | |
56 <conditional name="annotate"> | |
57 <param name="annotations" type="select" label="Select annotation"> | |
58 <option value="all" selected="true">All</option> | |
59 <option value="manual">Enter in text box</option> | |
60 <option value="auto">Scan pyGetGTFSources file</option> | |
61 </param> | |
62 <when value="all"> | |
63 <param name="annotation" type="hidden" format="txt" size="10" value="all"/> | |
64 </when> | |
65 <when value="manual"> | |
66 <param name="annotation" type="text" format="txt" size="100" value="protein_coding" label="Select which annotation to focus search on --annotation" help="To find a list of available annotations please use pyGetGTFSources tool"> | |
67 <validator type="empty_field" message="Please enter a value"/> | |
68 </param> | |
69 </when> | |
70 <when value="auto"> | |
71 <param format="tabular" name="gtf_annotation" type="data" label="GTF annotation File (pyGetGTFSources output)" help="Tabular file containing unique list of annotations/sources in selected GTF file. Refer to pyGetGTFSources"/> | |
72 <conditional name="scan"> | |
73 <param name="annotations" type="select" label="Scan this file for annotations" help="Choose the correct GTF file then choose GO"> | |
74 <option value="wait" selected="true">Waiting</option> | |
75 <option value="scanning">Go</option> | |
76 </param> | |
77 <when value="wait"> | |
78 </when> | |
79 <when value="scanning"> | |
80 <param name="annotation" type="select" multiple="false" label="Select which annotation to focus search on --annotation"> | |
81 <options from_dataset="gtf_annotation"> | |
82 <column name="name" index="0"/> | |
83 <column name="value" index="0"/> | |
84 </options> | |
85 </param> | |
86 </when> | |
87 </conditional> | |
88 </when> | |
89 </conditional> | |
90 | |
91 </when> | |
92 <when value="other"> | |
93 <param format="gtf" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/> | |
94 <conditional name="annotate"> | |
95 <param name="annotations" type="select" label="Select annotation"> | |
96 <option value="all" selected="true">All</option> | |
97 <option value="manual">Enter in text box</option> | |
98 <option value="auto">Scan selected file</option> | |
99 </param> | |
100 <when value="all"> | |
101 <param name="annotation" type="hidden" format="txt" size="10" value="all"/> | |
102 </when> | |
103 <when value="manual"> | |
104 <param name="annotation" type="text" format="txt" size="100" value="protein_coding" label="Select which annotation to focus search on --annotation" help="To find a list of available annotations please use pyGetGTFSources tool"> | |
105 <validator type="empty_field" message="Please enter a value"/> | |
106 </param> | |
107 </when> | |
108 <when value="auto"> | |
109 <param name="annotation" type="select" multiple="false" label="Select which annotation to focus search on --annotation"> | |
110 <options from_dataset="gtf"> | |
111 <column name="name" index="1"/> | |
112 <column name="value" index="1"/> | |
113 <filter type="unique_value" name="unique" column="1"/> | |
114 </options> | |
115 </param> | |
116 </when> | |
117 </conditional> | |
118 </when> | |
119 </conditional> | |
120 | |
121 | |
122 <conditional name="addOpt"> | |
123 <param name="options" type="select" label="Options"> | |
124 <option value="default" selected="true">Default</option> | |
125 <option value="edit">Edit</option> | |
126 </param> | |
127 <when value="edit"> | |
128 <param format="integer" name="range" type="integer" label="Range --range" value="0" size="5" help="Manually set the length of the 5' and 3' UTRs 0>50000"> | |
129 <validator type="in_range" min="0" max="50000" message="Please enter a value between 0 and 50000"/> | |
130 </param> | |
131 <param format="integer" name="numberofbins" type="integer" label="Set the number of bins --numberofbins" value="20" size="7" help="Set the number of bins you want to divide the genes into"> | |
132 <validator type="in_range" min="20" max="1000" message="Please enter a value between 20 and 1000"/> | |
133 </param> | |
134 <param format="integer" name="min_length" type="integer" label="Set the minimum gene length (nt) --min_length" value="50" size="7" help="To filter the data for gene length (nucleotides)" > | |
135 <validator type="in_range" min="20" message="Please enter a value greater than 20"/> | |
136 </param> | |
137 <param format="integer" name="max_length" type="integer" label="Set the maximum gene length (nt) --max_length" help="Default = 100000000" value="100000000" size="10" > | |
138 <validator type="in_range" min="50" max="100000000" message="Please enter a value between 50 and 100000000"/> | |
139 </param> | |
140 <param name="sequence" type="select" label="What sequences do you want to run pyBinCollector on? --sequence"> | |
141 <option value="genomic" selected="true">Genomic Sequence</option> | |
142 <option value="coding">Coding Sequence</option> | |
143 <option value="intron">Introns</option> | |
144 <option value="exon">Exons</option> | |
145 <option value="CDS">CDS</option> | |
146 <option value="5UTR">5UTR</option> | |
147 <option value="3UTR">3UTR</option> | |
148 </param> | |
149 <conditional name="limitBins"> | |
150 <param name="binselect" type="select" label="Select sequences that map to specific bins --binselect"> | |
151 <option value="no" selected="true">No</option> | |
152 <option value="yes">Yes</option> | |
153 </param> | |
154 <when value="yes"> | |
155 <param format="integer" name="bs_first" type="integer" label="Select First Bin" value="1" size="7"> | |
156 <validator type="in_range" min="1" message="Please enter a value greater than 0"/> | |
157 </param> | |
158 <param format="integer" name="bs_last" type="integer" label="Select Last Bin" value="2" size="7"> | |
159 <validator type="in_range" min="2" message="Please enter a value greater than 0"/> | |
160 </param> | |
161 </when> | |
162 <when value="no"> | |
163 </when> | |
164 </conditional> | |
165 <param name="ignore" type="select" label="Ignore strand information? --ignorestrand"> | |
166 <option value="" selected="true">No</option> | |
167 <option value="--ignorestrand">Yes</option> | |
168 </param> | |
169 <conditional name="oall"> | |
170 <param name="outputall" type="select" label="Output all genes --outputall" help="output the normalized distribution for each individual gene, rather than making a cumulative coverage plot"> | |
171 <option value="" selected="true">No</option> | |
172 <option value="--outputall">Yes</option> | |
173 </param> | |
174 <when value="--outputall"/> | |
175 <when value=""/> | |
176 </conditional> | |
177 </when> | |
178 <when value="default"> | |
179 </when> | |
180 </conditional> | |
181 <param name="label" type="text" format="txt" size="30" value="pyBinCollector" label="Enter output file label -o" /> | |
182 </inputs> | |
183 | |
184 <outputs> | |
185 <data format="gtf" name="out" label="${label.value}.gtf"> | |
186 <filter>addOpt['oall']['outputall'] == ""</filter> | |
187 </data> | |
188 <data format="txt" name="sd" label="sense_data_${label.value}.txt"> | |
189 <filter>addOpt['options'] == "edit" and addOpt['oall']['outputall'] == "--outputall"</filter> | |
190 </data> | |
191 <data format="txt" name="ssub" label="sense_subs_${label.value}.txt"> | |
192 <filter>addOpt['options'] == "edit" and addOpt['oall']['outputall'] == "--outputall"</filter> | |
193 </data> | |
194 <data format="txt" name="sdel" label="sense_dels_${label.value}.txt"> | |
195 <filter>addOpt['options'] == "edit" and addOpt['oall']['outputall'] == "--outputall"</filter> | |
196 </data> | |
197 <data format="txt" name="asd" label="anti_sense_data_${label.value}.txt"> | |
198 <filter>addOpt['options'] == "edit" and addOpt['oall']['outputall'] == "--outputall"</filter> | |
199 </data> | |
200 <data format="txt" name="assub" label="anti_sense_subs_${label.value}.txt"> | |
201 <filter>addOpt['options'] == "edit" and addOpt['oall']['outputall'] == "--outputall"</filter> | |
202 </data> | |
203 <data format="txt" name="asdel" label="anti_sense_dels_${label.value}.txt"> | |
204 <filter>addOpt['options'] == "edit" and addOpt['oall']['outputall'] == "--outputall"</filter> | |
205 </data> | |
206 </outputs> | |
207 <help> | |
208 | |
209 | |
210 .. class:: infomark | |
211 | |
212 **pyBinCollector** | |
213 | |
214 pyBinCollector is part of the pyCRAC_ package. Allows the user to generate genome-wide coverage plots. Normalises gene lengths by dividing genes into a | |
215 fixed number of bins and then calculates the hit density in each bin. The program also allows the user to input specific bin numbers to extract | |
216 blocks/clusters present in these bins. | |
217 | |
218 | |
219 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html | |
220 | |
221 ------ | |
222 | |
223 **Parameter list** | |
224 | |
225 File input options:: | |
226 | |
227 -f FILE, --input_file=FILE | |
228 Provide the path and name of the pyReadCounters.py or | |
229 pyMotif.py GTF file. By default the program expects | |
230 data from the standard input. | |
231 -o OUTPUT_FILE, --output_file=OUTPUT_FILE | |
232 To set an output file name. Do not add a file | |
233 extension. By default, if the --outputall flag is not | |
234 used, the program writes to the standard output. | |
235 --gtf=yeast.gtf | |
236 type the path to the gtf annotation file that you want | |
237 to use. Default is /usr/local/pyCRAC/db/Saccharomyces_ | |
238 cerevisiae.EF2.59.1.2.gtf | |
239 | |
240 pyBinCollector.py specific options:: | |
241 | |
242 -a protein_coding, --annotation=protein_coding | |
243 select which annotation (i.e. protein_coding, ncRNA, | |
244 sRNA, rRNA, tRNA, snoRNA, all) you would like to focus | |
245 your search on. Default = all | |
246 --min_length=20 | |
247 to set a minimum length threshold for genes. Genes | |
248 shorter than the minimal length will be discarded. | |
249 Default = 1 | |
250 --max_length=10000 | |
251 to set a maximum length threshold for genes. Genes | |
252 larger than the maximum length will be discarded. | |
253 Default = 100000000 | |
254 -n 20, --numberofbins=20 | |
255 select the number of bins you want to generate. | |
256 Default=20 | |
257 --binselect=2 4 | |
258 allows selection of sequences that were mapped to | |
259 specific bins. This option expects two numbers, one | |
260 for each bin, separated by a space. For example: | |
261 --binselect 20 30. | |
262 --outputall | |
263 use this flag to output the normalized distribution | |
264 for each individual gene, rather than making a | |
265 cumulative coverage plot. Useful for making box plots | |
266 or for making heat maps. | |
267 | |
268 Common options:: | |
269 | |
270 -r 100, --range=100 | |
271 allows you to set the length of the UTR regions. If | |
272 you set '-r 50' or '--range=50', then the program will | |
273 set a fixed length (50 bp) regardless of whether the | |
274 GTF file has genes with annotated UTRs. | |
275 -s intron, --sequence=intron | |
276 with this option you can select whether you want to | |
277 generate bins from the coding or genomic sequence or | |
278 introns,exon,CDS, or UTR coordinates. Default = | |
279 genomic | |
280 --ignorestrand | |
281 To ignore strand information and all reads overlapping | |
282 with genomic features will be considered sense reads. | |
283 Useful for analysing ChIP or RIP data | |
284 | |
285 | |
286 | |
287 | |
288 | |
289 </help> | |
290 </tool> |