Mercurial > repos > bgruening > bismark
comparison bismark_bowtie2_wrapper.xml @ 9:1a88b0f2669f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 5da44021266ae8cd3cdffc045ae53490e2a59a05
| author | bgruening |
|---|---|
| date | Fri, 22 Feb 2019 14:15:46 -0500 |
| parents | 9bfe38410155 |
| children | 7bffcb6fc81d |
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| 8:9bfe38410155 | 9:1a88b0f2669f |
|---|---|
| 1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0" profile="18.01"> | 1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0.1" 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> |
| 99 | 99 |
| 100 ## if set, disable the original behaviour | 100 ## if set, disable the original behaviour |
| 101 $params.no_mixed | 101 $params.no_mixed |
| 102 ## if set, disable the original behaviour | 102 ## if set, disable the original behaviour |
| 103 $params.no_discordant | 103 $params.no_discordant |
| 104 | |
| 105 $params.non_directional | |
| 104 | 106 |
| 105 #if $params.bismark_stdout: | 107 #if $params.bismark_stdout: |
| 106 --stdout '$output_stdout' | 108 --stdout '$output_stdout' |
| 107 #end if | 109 #end if |
| 108 | 110 |
| 248 <!-- output Options --> | 250 <!-- output Options --> |
| 249 <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" |
| 250 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"/> |
| 251 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true" | 253 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true" |
| 252 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" type="boolean" truevalue="--non_directional" falsevalue="" checked="false" | |
| 256 label="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported."/> | |
| 253 | 257 |
| 254 <!--end output options --> | 258 <!--end output options --> |
| 255 </when> <!-- full --> | 259 </when> <!-- full --> |
| 256 </conditional> <!-- params --> | 260 </conditional> <!-- params --> |
| 257 <!-- | 261 <!-- |