Mercurial > repos > jackcurragh > ribogalaxy_bowtie_rrna
comparison bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.xml @ 22:ca7c965f7cc9 draft
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| author | jackcurragh |
|---|---|
| date | Thu, 12 May 2022 14:15:48 +0000 |
| parents | b49ad9f12dfa |
| children | ef1a6b28b664 |
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| 21:b49ad9f12dfa | 22:ca7c965f7cc9 |
|---|---|
| 1 <tool id="bowtie_rRNA_tRNA_removal_wrapper" name="Remove rRNA and tRNA using Bowtie" version="1.5.0"> | 1 <tool id="bowtie_rRNA_tRNA_removal_wrapper" name="Remove rRNA and tRNA using Bowtie" version="1.5.0"> |
| 2 <description></description> | 2 <description></description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.2.0">bowtie</requirement> | 4 <requirement type="package" version="1.3.0">bowtie</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <version_command>bowtie --version</version_command> | 6 <version_command>bowtie --version</version_command> |
| 7 <command> | 7 <command> |
| 8 python '$__tool_directory__/bowtie_rRNA_tRNA_removal_wrapper.py' | 8 python '$__tool_directory__/bowtie_rRNA_tRNA_removal_wrapper.py' |
| 9 ## Set number of threads | 9 ## Set number of threads |
| 418 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> | 418 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> |
| 419 </when> <!-- full --> | 419 </when> <!-- full --> |
| 420 </conditional> <!-- pParams --> | 420 </conditional> <!-- pParams --> |
| 421 </when> <!-- paired --> | 421 </when> <!-- paired --> |
| 422 </conditional> <!-- singlePaired --> | 422 </conditional> <!-- singlePaired --> |
| 423 <param name="save_mapped_reads" type="boolean" checked="False" label="Same the bowtie alignments to the non-coding RNA" /> | 423 <param name="save_mapped_reads" type="boolean" checked="False" label="Save the bowtie alignments to the non-coding RNA" /> |
| 424 <param name="save_mapping_stats" type="boolean" checked="True" label="Save the bowtie mapping statistics to the history" /> | 424 <param name="save_mapping_stats" type="boolean" checked="True" label="Save the bowtie mapping statistics to the history" /> |
| 425 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" /> | 425 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" /> |
| 426 </inputs> | 426 </inputs> |
| 427 <outputs> | 427 <outputs> |
| 428 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> | 428 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> |