Mercurial > repos > bgruening > bismark

comparison bismark_bowtie2_wrapper.xml @ 11:1f15ad5ca867 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/bismark commit 56a53a4dd68f1472ec256d3a8b2a44afc24018a4
author bgruening
date Thu, 02 May 2019 18:27:38 -0400
parents 7bffcb6fc81d
children f211753166bd
comparison
equal deleted inserted replaced
10:7bffcb6fc81d 11:1f15ad5ca867
1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0.2" profile="18.01"> 1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0.3" profile="18.01">
2 <description>Bisulfite reads mapper</description> 2 <description>Bisulfite reads mapper</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.20.0">bismark</requirement> 4 <requirement type="package" version="0.20.0">bismark</requirement>
5 <requirement type="package" version="1.8">samtools</requirement> 5 <requirement type="package" version="1.8">samtools</requirement>
6 <requirement type="package" version="2.3.4.2">bowtie2</requirement> 6 <requirement type="package" version="2.3.4.2">bowtie2</requirement>
209 help="You can use the default settings or set custom values for any of Bismark's parameters."> 209 help="You can use the default settings or set custom values for any of Bismark's parameters.">
210 <option value="default">Use Defaults</option> 210 <option value="default">Use Defaults</option>
211 <option value="custom">Full parameter list</option> 211 <option value="custom">Full parameter list</option>
212 </param> 212 </param>
213 <!-- Full/advanced params. --> 213 <!-- Full/advanced params. -->
214 <when value="dafault"></when> 214 <when value="default"></when>
215 <when value="custom"> 215 <when value="custom">
216 <!-- -N --> 216 <!-- -N -->
217 <param name="seed_mismatches" type="integer" value="0" 217 <param name="seed_mismatches" type="integer" value="0"
218 label="Number of mismatches to be allowed in a seed alignment during multiseed alignment"/> 218 label="Number of mismatches to be allowed in a seed alignment during multiseed alignment"/>
219 <!-- -L --> 219 <!-- -L -->
251 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" 251 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false"
252 label="Write the bismark output and summary information to an extra file"/> 252 label="Write the bismark output and summary information to an extra file"/>
253 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true" 253 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true"
254 label="Offer all report files concatenated in one file (Mapping Report)"/> 254 label="Offer all report files concatenated in one file (Mapping Report)"/>
255 <param argument="--non-directional" name="non_directional" type="boolean" 255 <param argument="--non-directional" name="non_directional" type="boolean"
256 truevalue="--non-directional" falsevalue="" checked="false" 256 truevalue="--non-directional" falsevalue="" checked="false"
257 label="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported."/> 257 label="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported."/>
258 258
259 <!--end output options --> 259 <!--end output options -->
260 </when> <!-- full --> 260 </when> <!-- full -->
261 </conditional> <!-- params --> 261 </conditional> <!-- params -->