Mercurial > repos > jackcurragh > ribogalaxy_bowtie_transcriptome
comparison bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml @ 24:65e9b881213b draft default tip
Uploaded
| author | jackcurragh |
|---|---|
| date | Mon, 27 Mar 2023 09:53:42 +0000 |
| parents | 1157b2d3f288 |
| children |
comparison
equal
deleted
inserted
replaced
| 23:1157b2d3f288 | 24:65e9b881213b |
|---|---|
| 1 <tool id="bowtie_trans_wrapper" name="Bowtie Transcriptome Alignment" version="1.8c"> | 1 <tool id="bowtie_trans_wrapper" name="Bowtie Transcriptome Alignment" version="1.7.7"> |
| 2 <description>Align to Transcriptome using Bowtie</description> | 2 <description>Align to Transcriptome using Bowtie</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.2.0">bowtie</requirement> | 4 <requirement type="package" version="1.2.0">bowtie</requirement> |
| 5 <requirement type="package" version="1.13">samtools</requirement> | 5 <requirement type="package" version="1.13">samtools</requirement> |
| 6 | 6 |
| 424 </conditional> <!-- singlePaired --> | 424 </conditional> <!-- singlePaired --> |
| 425 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" /> | 425 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" /> |
| 426 <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 <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" /> |
| 427 </inputs> | 427 </inputs> |
| 428 <outputs> | 428 <outputs> |
| 429 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> | 429 <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads"> |
| 430 <actions> | 430 <actions> |
| 431 <conditional name="refGenomeSource.genomeSource"> | 431 <conditional name="refGenomeSource.genomeSource"> |
| 432 <when value="indexed"> | 432 <when value="indexed"> |
| 433 <action type="metadata" name="dbkey"> | 433 <action type="metadata" name="dbkey"> |
| 434 <option type="from_data_table" name="bowtie_transcriptome_indexes_4" column="1" offset="0"> | 434 <option type="from_data_table" name="bowtie_transcriptome_indexes_4" column="1" offset="0"> |