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comparison MethylDackel.xml @ 7:15df15127c18 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c
author bgruening
date Fri, 23 Mar 2018 17:52:57 -0400
parents 906db57d5d65
children d6787bab7b11
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6:906db57d5d65 7:15df15127c18
1 <tool id="pileometh" name="MethylDackel" version="0.3.0"> 1 <tool id="pileometh" name="MethylDackel" version="0.3.0.1">
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="0.3.0">methyldackel</requirement> 4 <requirement type="package" version="0.3.0">methyldackel</requirement>
5 </requirements> 5 </requirements>
6 <stdio>
7 <!-- Anything other than zero is an error -->
8 <exit_code range="1:" />
9 <exit_code range=":-1" />
10 <!-- In case the return code has not been set propery check stderr too -->
11 <regex match="Error:" />
12 <regex match="Exception:" />
13 </stdio>
14 <version_command><![CDATA[MethylDackel --version]]></version_command> 6 <version_command><![CDATA[MethylDackel --version]]></version_command>
15 <command><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
16 #if $reference_source.reference_source_selector == "cached": 8 #if $reference_source.reference_source_selector == "cached":
17 ln -s $reference_source.ref_file.fields.path reference.fasta && 9 ln -s $reference_source.ref_file.fields.path reference.fasta &&
18 #else: 10 #else:
19 ln -s $reference_source.ref_file reference.fasta && 11 ln -s $reference_source.ref_file reference.fasta &&
20 #end if 12 #end if
41 #end if 33 #end if
42 34
43 #if $advanced_options.options=="yes": 35 #if $advanced_options.options=="yes":
44 #if $advanced_options.mbias_regionString: 36 #if $advanced_options.mbias_regionString:
45 -r $advanced_options.mbias_regionString 37 -r $advanced_options.mbias_regionString
38 #end if
39 #if $advanced_options.regionBed:
40 -l '$advanced_options.regionBed'
46 #end if 41 #end if
47 $advanced_options.keepDupes 42 $advanced_options.keepDupes
48 $advanced_options.keepSingleton 43 $advanced_options.keepSingleton
49 $advanced_options.keepDiscordant 44 $advanced_options.keepDiscordant
50 -q $advanced_options.min_mapq 45 -q $advanced_options.min_mapq
73 --nCTOB $advanced_options.nCTOB 68 --nCTOB $advanced_options.nCTOB
74 #end if 69 #end if
75 #end if 70 #end if
76 $advanced_options.CHG 71 $advanced_options.CHG
77 $advanced_options.CHH 72 $advanced_options.CHH
73 $advanced_options.noCpG
78 #end if 74 #end if
79 75
80 reference.fasta 76 reference.fasta
81 77
82 $input_sortedAlignBAM 78 $input_sortedAlignBAM
83 79
84 #if $main_task.task == "mbias": 80 #if $main_task.task == "mbias":
85 out_mbias && 81 out_mbias $main_task.tsv > out_mbias.tsv &&
86 touch out_mbias_OT.svg && 82 touch out_mbias_OT.svg &&
87 touch out_mbias_OB.svg && 83 touch out_mbias_OB.svg &&
88 touch out_mbias_CTOT.svg && 84 touch out_mbias_CTOT.svg &&
89 touch out_mbias_CTOB.svg 85 touch out_mbias_CTOB.svg
90 #end if 86 #end if
129 example by using the MBias program." /> 125 example by using the MBias program." />
130 <param name="OB" type="text" value="" label="Original bottom strand bounds (comma-separated, no spaces)" /> 126 <param name="OB" type="text" value="" label="Original bottom strand bounds (comma-separated, no spaces)" />
131 <param name="CTOT" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" /> 127 <param name="CTOT" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" />
132 <param name="CTOB" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" /> 128 <param name="CTOB" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" />
133 </when> 129 </when>
134 <when value="mbias"/> 130 <when value="mbias">
131 <param name="tsv" type="boolean" truevalue="--txt" falsevalue=""
132 label="output tab separated mbias metrics"/>
133 </when>
135 </conditional> 134 </conditional>
136 <conditional name="advanced_options"> 135 <conditional name="advanced_options">
137 <param name="options" type="select" label="Advanced options"> 136 <param name="options" type="select" label="Advanced options">
138 <option value="">Hide advanced options</option> 137 <option value="">Hide advanced options</option>
139 <option value="yes">Display advanced options</option> 138 <option value="yes">Display advanced options</option>
140 </param> 139 </param>
141 <when value="yes"> 140 <when value="yes">
142 <param name="mbias_regionString" type="text" value="" label="Region string in which to extract methylation"/> 141 <param name="mbias_regionString" type="text" value="" label="Region string in which to extract methylation (e.g. chr1:1-100)"/>
142 <param name="regionBed" type="data" optional="true" format='bed' label="Bed file of regions for inclusion"/>
143 <param name="keepDupes" type="boolean" checked="false" truevalue="--keepDupes" falsevalue="" 143 <param name="keepDupes" type="boolean" checked="false" truevalue="--keepDupes" falsevalue=""
144 label="By default, any alignment marked as a duplicate is ignored. This option causes them to be incorporated" /> 144 label="By default, any alignment marked as a duplicate is ignored. This option causes them to be incorporated" />
145 <param name="keepSingleton" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue="" 145 <param name="keepSingleton" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue=""
146 label="By default, if only one read in a pair aligns (a singleton) then it's ignored." /> 146 label="By default, if only one read in a pair aligns (a singleton) then it's ignored." />
147 <param name="keepDiscordant" type="boolean" checked="false" truevalue="--keepDiscordant" falsevalue="" 147 <param name="keepDiscordant" type="boolean" checked="false" truevalue="--keepDiscordant" falsevalue=""
148 label="By default, paired-end alignments with the properly-paired bit unset in the FLAG field are ignored. Note that the definition of concordant and discordant is based on your aligner settings." /> 148 label="By default, paired-end alignments with the properly-paired bit unset in the FLAG field are ignored. Note that the definition of concordant and discordant is based on your aligner settings." />
149 <param name="min_mapq" type="integer" value="10" label="Minimum MAPQ threshold to include an alignment (default 10)"/> 149 <param name="min_mapq" type="integer" value="10" label="Minimum MAPQ threshold to include an alignment (default 10)"/>
150 <param name="min_phred" type="integer" value="5" label="Minimum Phred threshold to include a base (default 5). This must be >0."/> 150 <param name="min_phred" type="integer" value="5" label="Minimum Phred threshold to include a base (default 5). This must be >0."/>
151 <param name="max_pbdepth" type="integer" value="2000" label="Maximum per-base depth (default 2000)"/> 151 <param name="max_pbdepth" type="integer" value="2000" label="Maximum per-base depth (default 2000)"/>
152 <param name="min_pbdepth" type="integer" value="1" min="1" label="Minimum per-base depth" 152 <param name="min_pbdepth" type="integer" value="1" min="1" label="Minimum per-base depth"
153 help="Minimum per-base dpeth for reporting output. If you use --mergeContext (above), then this applies to the merged CpG/CHG (default 1). (-d)" /> 153 help="Minimum per-base depth for reporting output. If you use --mergeContext (above), then this applies to the merged CpG/CHG (default 1). (-d)" />
154 154
155 <param name="ignoreFlags" type="integer" value="3840" label="Ignore certain alignments" 155 <param name="ignoreFlags" type="integer" value="3840" label="Ignore certain alignments"
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." /> 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." />
157 <param name="requireFlags" type="integer" value="0" label="Require alignment flags" 157 <param name="requireFlags" type="integer" value="0" label="Require alignment flags"
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." /> 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." />
168 <param name="logit" type="boolean" checked="false" truevalue="--logit" falsevalue="" 168 <param name="logit" type="boolean" checked="false" truevalue="--logit" falsevalue=""
169 label="Extract logit(M/(M+U)) (only) at each position. This is mutually exclusive with --counts, --fraction, and --methylKit" /> 169 label="Extract logit(M/(M+U)) (only) at each position. This is mutually exclusive with --counts, --fraction, and --methylKit" />
170 <param name="methylKit" type="boolean" checked="false" truevalue="--methylKit" falsevalue="" 170 <param name="methylKit" type="boolean" checked="false" truevalue="--methylKit" falsevalue=""
171 label="Output in the format required by methylKit. This is mutually exclusive with --counts, --fraction, and --logit" /> 171 label="Output in the format required by methylKit. This is mutually exclusive with --counts, --fraction, and --logit" />
172 172
173 <param name="noCpG" type="boolean" checked="false" truevalue="--noCpG" falsevalue=""
174 label="Do not output CpG context methylation metrics" />
173 <param name="CHG" type="boolean" checked="false" truevalue="--CHG" falsevalue="" 175 <param name="CHG" type="boolean" checked="false" truevalue="--CHG" falsevalue=""
174 label="Additional output file with CHG methylation metrics" /> 176 label="Output CHG context methylation metrics" />
175 <param name="CHH" type="boolean" checked="false" truevalue="--CHH" falsevalue="" 177 <param name="CHH" type="boolean" checked="false" truevalue="--CHH" falsevalue=""
176 label="Additional output file with CHH methylation metrics" /> 178 label="Output CHH context methylation metrics" />
177 179
178 <param name="nOT" type="text" value="" label="Original top strand absolute bounds (comma-separated, no spaces)" 180 <param name="nOT" type="text" value="" label="Original top strand absolute bounds (comma-separated, no spaces)"
179 help="Like --OT, but always exclude INT bases from a given end 181 help="Like --OT, but always exclude INT bases from a given end
180 from inclusion,regardless of the length of an alignment. This 182 from inclusion,regardless of the length of an alignment. This
181 is useful in cases where reads may have already been trimmed 183 is useful in cases where reads may have already been trimmed
194 <filter>main_task['task'] == "extract"</filter> 196 <filter>main_task['task'] == "extract"</filter>
195 <filter>not advanced_options['logit']</filter> 197 <filter>not advanced_options['logit']</filter>
196 <filter>not advanced_options['methylKit']</filter> 198 <filter>not advanced_options['methylKit']</filter>
197 <filter>not advanced_options['counts']</filter> 199 <filter>not advanced_options['counts']</filter>
198 <filter>not advanced_options['fraction']</filter> 200 <filter>not advanced_options['fraction']</filter>
201 <filter>not advanced_options['noCpG']</filter>
199 </data> 202 </data>
200 <data name="outFileExtractCpGLogit" format="bedgraph" from_work_dir="output_CpG.logit.bedGraph" 203 <data name="outFileExtractCpGLogit" format="bedgraph" from_work_dir="output_CpG.logit.bedGraph"
201 label="${tool.name} on ${on_string} (logit)"> 204 label="${tool.name} on ${on_string} (logit)">
202 <filter>main_task['task'] == "extract" and advanced_options['logit']</filter> 205 <filter>main_task['task'] == "extract" and advanced_options['logit']</filter>
203 </data> 206 </data>
279 label="${tool.name} on ${on_string} (CHH fraction)"> 282 label="${tool.name} on ${on_string} (CHH fraction)">
280 <filter>main_task['task'] == "extract" and advanced_options['fraction']</filter> 283 <filter>main_task['task'] == "extract" and advanced_options['fraction']</filter>
281 <filter>advanced_options['options'] == "yes"</filter> 284 <filter>advanced_options['options'] == "yes"</filter>
282 <filter>advanced_options['CHH']</filter> 285 <filter>advanced_options['CHH']</filter>
283 </data> 286 </data>
287 <data name="outFileMbiasTSV" format="tabular" from_work_dir="out_mbias.tsv"
288 label="${tool.name} on ${on_string} (methylation bias, tsv)">
289 <filter>main_task['task'] == 'mbias'</filter>
290 <filter>main_task['tsv']</filter>
291 </data>
284 <data name="outFileMbiasCpGOT" format="svg" from_work_dir="out_mbias_OT.svg" 292 <data name="outFileMbiasCpGOT" format="svg" from_work_dir="out_mbias_OT.svg"
285 label="${tool.name} on ${on_string} (methylation bias, original top strand)"> 293 label="${tool.name} on ${on_string} (methylation bias, original top strand)">
286 <filter>main_task['task'] == 'mbias'</filter> 294 <filter>main_task['task'] == 'mbias'</filter>
287 </data> 295 </data>
288 <data name="outFileMbiasCpGOB" format="svg" from_work_dir="out_mbias_OB.svg" 296 <data name="outFileMbiasCpGOB" format="svg" from_work_dir="out_mbias_OB.svg"
358 <param name="ref_file" value="cg100.fa" ftype="fasta" /> 366 <param name="ref_file" value="cg100.fa" ftype="fasta" />
359 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/> 367 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
360 <param name="options" value="yes"/> 368 <param name="options" value="yes"/>
361 <param name="methylKit" value="true" /> 369 <param name="methylKit" value="true" />
362 <output name="outFileExtractCpGMethylKit" file="test_5.methylKit" ftype="text" compare="diff"/> 370 <output name="outFileExtractCpGMethylKit" file="test_5.methylKit" ftype="text" compare="diff"/>
371 </test>
372 <test>
373 <param name="task" value="mbias" />
374 <param name="min_mapq" value="2" />
375 <param name="options" value="yes"/>
376 <param name="tsv" value="--txt"/>
377 <param name="reference_source_selector" value="history" />
378 <param name="ref_file" value="cg100.fa" ftype="fasta" />
379 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
380 <output name="outFileMbiasTSV" file="test7_output.tsv" ftype="tabular" compare="diff"/>
381 </test>
382 <test>
383 <param name="task" value="mbias" />
384 <param name="min_mapq" value="2" />
385 <param name="options" value="yes"/>
386 <param name="regionBed" ftype="bed" value="cg100.bed"/>
387 <param name="tsv" value="--txt"/>
388 <param name="reference_source_selector" value="history" />
389 <param name="ref_file" value="cg100.fa" ftype="fasta" />
390 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
391 <output name="outFileMbiasTSV" file="test8_output.tsv" ftype="tabular" compare="diff"/>
363 </test> 392 </test>
364 </tests> 393 </tests>
365 <help><![CDATA[ 394 <help><![CDATA[
366 395
367 .. image:: $PATH_TO_IMAGES/MethylDackelLogo.png 396 .. image:: $PATH_TO_IMAGES/MethylDackelLogo.png