Mercurial > repos > bgruening > pileometh

comparison PileOMeth.xml @ 2:cda51d96a9bc draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit bff5ba839e2cb63792b0d25018460d76eb398002
author bgruening
date Mon, 13 Feb 2017 07:09:59 -0500
parents d1b66015effd
children
comparison
equal deleted inserted replaced
1:d1b66015effd 2:cda51d96a9bc
35 --CTOT $main_task.CTOT 35 --CTOT $main_task.CTOT
36 #end if 36 #end if
37 #if str($main_task.CTOB).strip() != "": 37 #if str($main_task.CTOB).strip() != "":
38 --CTOB $main_task.CTOB 38 --CTOB $main_task.CTOB
39 #end if 39 #end if
40 $main_task.keepSingleton
41 $main_task.keepDiscordant
42 $main_task.fraction
40 #end if 43 #end if
41 44
42 #if $advanced_options.options=="yes": 45 #if $advanced_options.options=="yes":
43 #if $advanced_options.mbias_regionString: 46 #if $advanced_options.mbias_regionString:
44 -r $advanced_options.mbias_regionString 47 -r $advanced_options.mbias_regionString
58 reference.fasta 61 reference.fasta
59 62
60 $input_sortedAlignBAM 63 $input_sortedAlignBAM
61 64
62 #if $main_task.task == "mbias": 65 #if $main_task.task == "mbias":
66 $main_task.keepSingleton_mbias
67 $main_task.keepDiscordant_mbias
63 out_mbias && 68 out_mbias &&
64 touch out_mbias_OT.svg && 69 touch out_mbias_OT.svg &&
65 touch out_mbias_OB.svg && 70 touch out_mbias_OB.svg &&
66 touch out_mbias_CTOT.svg && 71 touch out_mbias_CTOT.svg &&
67 touch out_mbias_CTOB.svg 72 touch out_mbias_CTOB.svg
106 strongly advised to consult a methylation bias plot, for 111 strongly advised to consult a methylation bias plot, for
107 example by using the MBias program." /> 112 example by using the MBias program." />
108 <param name="OB" type="text" value="" label="Original bottom strand bounds (comma-separated, no spaces)" /> 113 <param name="OB" type="text" value="" label="Original bottom strand bounds (comma-separated, no spaces)" />
109 <param name="CTOT" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" /> 114 <param name="CTOT" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" />
110 <param name="CTOB" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" /> 115 <param name="CTOB" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" />
111 </when> 116 <param name="keepSingleton" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue="" />
112 <when value="mbias"/> 117 <param name="keepDiscordant" type="boolean" checked="false" truevalue="--keepDiscordant" falsevalue="" />
118 <param name="fraction" type="boolean" checked="false" truevalue="--fraction" falsevalue="" />
119
120 </when>
121 <when value="mbias">
122 <param name="keepSingleton_mbias" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue="" />
123 <param name="keepDiscordant_mbias" type="boolean" checked="false" truevalue="--keepDiscordant" falsevalue="" />
124 </when>
113 </conditional> 125 </conditional>
114 <conditional name="advanced_options"> 126 <conditional name="advanced_options">
115 <param name="options" type="select" label="Advanced options"> 127 <param name="options" type="select" label="Advanced options">
116 <option value="">Hide advanced options</option> 128 <option value="">Hide advanced options</option>
117 <option value="yes">Display advanced options</option> 129 <option value="yes">Display advanced options</option>
143 </data> 155 </data>
144 <data name="outFileExtractCHG" format="bedgraph" from_work_dir="output_CHG.bedGraph" 156 <data name="outFileExtractCHG" format="bedgraph" from_work_dir="output_CHG.bedGraph"
145 label="${tool.name} on ${on_string} (CHG)"> 157 label="${tool.name} on ${on_string} (CHG)">
146 <filter>main_task['task'] == 'extract'</filter> 158 <filter>main_task['task'] == 'extract'</filter>
147 <filter>advanced_options['options'] == "yes"</filter> 159 <filter>advanced_options['options'] == "yes"</filter>
148 <filter>advanced_options['CHG'] == "--CHG"</filter> 160 <filter>advanced_options['CHG']</filter>
149 </data> 161 </data>
150 <data name="outFileExtractCHH" format="bedgraph" from_work_dir="output_CHH.bedGraph" 162 <data name="outFileExtractCHH" format="bedgraph" from_work_dir="output_CHH.bedGraph"
151 label="${tool.name} on ${on_string} (CHH)"> 163 label="${tool.name} on ${on_string} (CHH)">
152 <filter>main_task['task'] == 'extract'</filter> 164 <filter>main_task['task'] == 'extract'</filter>
153 <filter>advanced_options['options'] == "yes"</filter> 165 <filter>advanced_options['options'] == "yes"</filter>
154 <filter>advanced_options['CHH'] == "--CHH" </filter> 166 <filter>advanced_options['CHH']</filter>
155 </data> 167 </data>
156 <data name="outFileMbiasCpGOT" format="svg" from_work_dir="out_mbias_OT.svg" 168 <data name="outFileMbiasCpGOT" format="svg" from_work_dir="out_mbias_OT.svg"
157 label="${tool.name} on ${on_string} (methylation bias, original top strand)"> 169 label="${tool.name} on ${on_string} (methylation bias, original top strand)">
158 <filter>main_task['task'] == 'mbias'</filter> 170 <filter>main_task['task'] == 'mbias'</filter>
159 </data> 171 </data>
188 <param name="reference_source_selector" value="history" /> 200 <param name="reference_source_selector" value="history" />
189 <param name="ref_file" value="cg100.fa" ftype="fasta" /> 201 <param name="ref_file" value="cg100.fa" ftype="fasta" />
190 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/> 202 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
191 <output name="outFileMbiasCpG" file="test_2_output.svg" ftype="svg" compare="diff"/> 203 <output name="outFileMbiasCpG" file="test_2_output.svg" ftype="svg" compare="diff"/>
192 </test> 204 </test>
205 <test>
206 <param name="task" value="extract" />
207 <param name="min_mapq" value="2" />
208 <param name="options" value="yes"/>
209 <param name="CHH" value="True"/>
210 <param name="reference_source_selector" value="history" />
211 <param name="ref_file" value="cg100.fa" ftype="fasta" />
212 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
213 <param name="mergeContext" value="false"/>
214 <param name="options" value="yes"/>
215 <output name="outFileExtractCpG" file="test_1.bedGraph" ftype="bedgraph" compare="diff"/>
216 <output name="outFileExtractCHH" file="test_2.bedGraph" ftype="bedgraph" compare="diff"/>
217 </test>
193 </tests> 218 </tests>
194 <help><![CDATA[ 219 <help><![CDATA[
195 **What it does** 220 **What it does**
196 221
197 PileOMeth (using a PILEup to extract METHylation metrics) will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. PileOMeth requires an indexed fasta file containing the reference genome as well. 222 PileOMeth (using a PILEup to extract METHylation metrics) will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. PileOMeth requires an indexed fasta file containing the reference genome as well.