Mercurial > repos > bgruening > bismark
comparison bismark_bowtie2_wrapper.xml @ 23:4084128e7cca draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
| author | bgruening |
|---|---|
| date | Wed, 02 Sep 2015 15:55:46 -0400 |
| parents | 047eb877b6f0 |
| children |
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| 22:047eb877b6f0 | 23:4084128e7cca |
|---|---|
| 118 #end if | 118 #end if |
| 119 | 119 |
| 120 #if $params.isReportOutput: | 120 #if $params.isReportOutput: |
| 121 --output-report-file $report_file | 121 --output-report-file $report_file |
| 122 #end if | 122 #end if |
| 123 | |
| 124 $params.non_directional | |
| 123 | 125 |
| 124 #end if | 126 #end if |
| 125 | 127 |
| 126 ## | 128 ## |
| 127 ## Output parameters. | 129 ## Output parameters. |
| 218 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write ambiguous reads to an extra output file" help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely." /> | 220 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write ambiguous reads to an extra output file" help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely." /> |
| 219 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write all reads that could not be aligned to a file" /> | 221 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write all reads that could not be aligned to a file" /> |
| 220 <!-- output Options --> | 222 <!-- output Options --> |
| 221 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" /> | 223 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" /> |
| 222 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" /> | 224 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" /> |
| 225 | |
| 226 <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="false" label="Non strand-specific sequence library" | |
| 227 help="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported." /> | |
| 223 | 228 |
| 224 <!--end output options --> | 229 <!--end output options --> |
| 225 </when> <!-- full --> | 230 </when> <!-- full --> |
| 226 </conditional> <!-- params --> | 231 </conditional> <!-- params --> |
| 227 <!-- | 232 <!-- |