Mercurial > repos > bgruening > pileometh

comparison MethylDackel.xml @ 6:906db57d5d65 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d
author bgruening
date Tue, 13 Jun 2017 01:01:31 -0400
parents f112bf3dd5ff
children 15df15127c18
comparison
equal deleted inserted replaced
5:ccc755bdf11d 6:906db57d5d65
1 <tool id="pileometh" name="MethylDackel" version="0.2.1"> 1 <tool id="pileometh" name="MethylDackel" version="0.3.0">
2 <description>A tool for processing bisulfite sequencing alignments</description> 2 <description>A tool for processing bisulfite sequencing alignments</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.1">methyldackel</requirement> 4 <requirement type="package" version="0.3.0">methyldackel</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <!-- Anything other than zero is an error --> 7 <!-- Anything other than zero is an error -->
8 <exit_code range="1:" /> 8 <exit_code range="1:" />
9 <exit_code range=":-1" /> 9 <exit_code range=":-1" />
20 #end if 20 #end if
21 21
22 MethylDackel 22 MethylDackel
23 $main_task.task 23 $main_task.task
24 24
25 -@ \${GALAXY_SLOTS:-4}
25 #if $main_task.task == "extract": 26 #if $main_task.task == "extract":
26 -o output 27 -o output
27 $main_task.mergeContext 28 $main_task.mergeContext
28 #if str($main_task.OT).strip() != "": 29 #if str($main_task.OT).strip() != "":
29 --OT $main_task.OT 30 --OT $main_task.OT
48 $advanced_options.keepDiscordant 49 $advanced_options.keepDiscordant
49 -q $advanced_options.min_mapq 50 -q $advanced_options.min_mapq
50 -p $advanced_options.min_phred 51 -p $advanced_options.min_phred
51 -D $advanced_options.max_pbdepth 52 -D $advanced_options.max_pbdepth
52 #if $main_task.task == "extract": 53 #if $main_task.task == "extract":
54 --minOppositeDepth $advanced_options.minOppositeDepth
55 --maxVariantFrac $advanced_options.maxVariantFrac
53 -d $advanced_options.min_pbdepth 56 -d $advanced_options.min_pbdepth
54 --ignoreFlags $advanced_options.ignoreFlags 57 --ignoreFlags $advanced_options.ignoreFlags
55 --requireFlags $advanced_options.requireFlags 58 --requireFlags $advanced_options.requireFlags
56 $advanced_options.fraction 59 $advanced_options.fraction
57 $advanced_options.counts 60 $advanced_options.counts
151 154
152 <param name="ignoreFlags" type="integer" value="3840" label="Ignore certain alignments" 155 <param name="ignoreFlags" type="integer" value="3840" label="Ignore certain alignments"
153 help="By deault, any alignment marked as secondary (bit 0x100), failing QC (bit 0x200), a PCR/optical duplicate (0x400) or supplemental (0x800) is ignored. This equates to a value of 0xF00 or 3840 in decimal. If you would like to change that, you can specify a new value here." /> 156 help="By deault, any alignment marked as secondary (bit 0x100), failing QC (bit 0x200), a PCR/optical duplicate (0x400) or supplemental (0x800) is ignored. This equates to a value of 0xF00 or 3840 in decimal. If you would like to change that, you can specify a new value here." />
154 <param name="requireFlags" type="integer" value="0" label="Require alignment flags" 157 <param name="requireFlags" type="integer" value="0" label="Require alignment flags"
155 help="Require each alignment to have all bits in this value present, or else the alignment is ignored. This is equivalent to the -f option in samtools. The default is 0, which includes all alignments." /> 158 help="Require each alignment to have all bits in this value present, or else the alignment is ignored. This is equivalent to the -f option in samtools. The default is 0, which includes all alignments." />
159 <param name="minOppositeDepth" type="integer" value="0" min="0" label="Minimum depth for variant avoidance"
160 help="The minimum depth on the strand opposite of a C required to flag the position as possibly being a SNP. The default is 0 (ignore possible SNPs). Setting this to a value above 0 will cause the position to be ignored if a given fraction of non-G bases are present on the opposite strand and the overall coverage there is at least what is specified here." />
161 <param name="maxVariantFrac" type="float" value="1.0" min="0.0" max="1.0" label="Maximum tolerated variant fraction"
162 help="If the depth on the strand opposite of a C is at least that specified by 'Minimum depth for variant avoidance', and the fraction of non-G bases exceeds this value, then methylation extraction is skipped for this position." />
156 163
157 <param name="fraction" type="boolean" checked="false" truevalue="--fraction" falsevalue="" 164 <param name="fraction" type="boolean" checked="false" truevalue="--fraction" falsevalue=""
158 label="Extract fractional methylation (only) at each position. This is mutually exclusive with --counts, --logit, and --methylKit" /> 165 label="Extract fractional methylation (only) at each position. This is mutually exclusive with --counts, --logit, and --methylKit" />
159 <param name="counts" type="boolean" checked="false" truevalue="--counts" falsevalue="" 166 <param name="counts" type="boolean" checked="false" truevalue="--counts" falsevalue=""
160 label="Extract base counts (only) at each position. This is mutually exclusive with --fraction, --logit, and --methylKit" /> 167 label="Extract base counts (only) at each position. This is mutually exclusive with --fraction, --logit, and --methylKit" />
307 <param name="min_mapq" value="2" /> 314 <param name="min_mapq" value="2" />
308 <param name="options" value="yes"/> 315 <param name="options" value="yes"/>
309 <param name="reference_source_selector" value="history" /> 316 <param name="reference_source_selector" value="history" />
310 <param name="ref_file" value="cg100.fa" ftype="fasta" /> 317 <param name="ref_file" value="cg100.fa" ftype="fasta" />
311 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/> 318 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
312 <output name="outFileMbiasCpG" file="test_2_output.svg" ftype="svg" compare="diff"/> 319 <output name="outFileMbiasCpGOT" file="test_2_output.svg" ftype="svg" compare="diff"/>
313 </test> 320 </test>
314 <test> 321 <test>
315 <param name="task" value="extract" /> 322 <param name="task" value="extract" />
316 <param name="min_mapq" value="2" /> 323 <param name="min_mapq" value="2" />
317 <param name="options" value="yes"/> 324 <param name="options" value="yes"/>
439 446
440 **methylKit-compatible output** 447 **methylKit-compatible output**
441 448
442 methylKit has its own format, which can be produced with the `--methylKit` option. Merging Cs into CpGs or CHGs is forbidden in this format. Likewise, this option is mutually exclusive with `--logit` et al. 449 methylKit has its own format, which can be produced with the `--methylKit` option. Merging Cs into CpGs or CHGs is forbidden in this format. Likewise, this option is mutually exclusive with `--logit` et al.
443 450
451 **Excluding likely variant sites**
452
453 If your samples are not genetically homogenous, it can sometimes be advantageous to exclude likely variant sites from methylation extraction. As an example, since unmethylated Cs are read as Ts, extracting methylation from a position with a C->T mutation will cause incorrect results. In such a case, the opposite strand will have an A rather than a G (in the non-variant case, there would be a G regardless of methylation status). MethylDackel tracks the number of non-Gs on the strand opposite of Cs in the reference sequence. If the fraction of these exceeds the `--maxVariantFrac` option, then that position will be excluded from output. To exclude cases where the `--maxVariantFrac` value is exceeded only due to low coverage, the opposite strand must have a depth of coverage of at least `--minOppositeDepth`. Note that the default value for `--minOppositeDepth` is 0, indicating that the variant site exclusion process is skipped.
454
455 Note that if one additionally specifies `--mergeContext`, that a given CpG or CHG will be excluded from output if either of its individual Cs would be excluded given the specified `--minOppositeDepth` and `--maxVariantFrac`.
456
444 457
445 ----- 458 -----
446 459
447 **MethylDackel** is a Free and Open Source Software, see more details on the MethylDackel_ Website. 460 **MethylDackel** is a Free and Open Source Software, see more details on the MethylDackel_ Website.
448 461