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comparison bismark_methylation_extractor.xml @ 4:243e8f9fb75b draft

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author bgruening
date Mon, 09 Feb 2015 18:24:41 -0500
parents 91f07ff056ca
children b100248c35b8
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3:91f07ff056ca 4:243e8f9fb75b
7 <requirement type="package" version="0.12.8">bowtie</requirement> 7 <requirement type="package" version="0.12.8">bowtie</requirement>
8 <requirement type="package" version="2.1.0">bowtie2</requirement> 8 <requirement type="package" version="2.1.0">bowtie2</requirement>
9 </requirements> 9 </requirements>
10 <parallelism method="basic"></parallelism> 10 <parallelism method="basic"></parallelism>
11 <command interpreter="python"> 11 <command interpreter="python">
12 <![CDATA[
12 bismark_methylation_extractor.py 13 bismark_methylation_extractor.py
13 14
14 --infile $input 15 --infile $input
15 16
16 --bismark_path \$SCRIPT_PATH 17 #--bismark_path \$SCRIPT_PATH
17 18
18 #if $singlePaired.sPaired == "single": 19 #if $singlePaired.sPaired == "single":
19 --single-end 20 --single-end
20 #else: 21 #else:
21 --paired-end 22 --paired-end
76 --cpg_ctob $cpg_ctob 77 --cpg_ctob $cpg_ctob
77 #end if 78 #end if
78 ## end compress 79 ## end compress
79 #end if 80 #end if
80 81
82 ]]>
81 </command> 83 </command>
82 <inputs> 84 <inputs>
83 <!-- Input Parameters --> 85 <!-- Input Parameters -->
84 <param name="input" type="data" format="sam,bam" label="SAM/BAM file from Bismark bisulfite mapper" /> 86 <param name="input" type="data" format="sam,bam" label="SAM/BAM file from Bismark bisulfite mapper" />
85 <conditional name="singlePaired"> 87 <conditional name="singlePaired">
185 187
186 <tests> 188 <tests>
187 </tests> 189 </tests>
188 190
189 <help> 191 <help>
192 <![CDATA[
190 193
191 **What it does** 194 **What it does**
192 195
193 The following is a brief description of all options to control the Bismark_ 196 The following is a brief description of all options to control the Bismark_
194 methylation extractor. The script reads in a bisulfite read alignment results file 197 methylation extractor. The script reads in a bisulfite read alignment results file
195 produced by the Bismark bisulfite mapper and extracts the methylation information 198 produced by the Bismark bisulfite mapper and extracts the methylation information
196 for individual cytosines. This information is found in the methylation call field 199 for individual cytosines. This information is found in the methylation call field
197 which can contain the following characters: 200 which can contain the following characters:
198 201
199 202
283 methylation call string. This can remove e.g. a restriction enzyme site 286 methylation call string. This can remove e.g. a restriction enzyme site
284 at the start of each read. 287 at the start of each read.
285 288
286 Output:: 289 Output::
287 290
288 --comprehensive Specifying this option will merge all four possible strand-specific 291 --comprehensive Specifying this option will merge all four possible strand-specific
289 methylation info into context-dependent output files. The default 292 methylation info into context-dependent output files. The default
290 contexts are: 293 contexts are:
291 - CpG context 294 - CpG context
292 - CHG context 295 - CHG context
293 - CHH context 296 - CHH context
294 297
299 302
300 --report Prints out a short methylation summary as well as the paramaters used to run 303 --report Prints out a short methylation summary as well as the paramaters used to run
301 this script. 304 this script.
302 305
303 306
307 ]]>
304 </help> 308 </help>
305 </tool> 309 </tool>