Mercurial > repos > jackcurragh > ribogalaxy_bowtie_genome
comparison bowtie_genome_wrapper/bowtie_genomic_wrapper.xml @ 14:a1565147cdc8 draft default tip
Uploaded
| author | jackcurragh |
|---|---|
| date | Mon, 27 Mar 2023 09:38:54 +0000 |
| parents | e8551e16829c |
| children |
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| 13:e8551e16829c | 14:a1565147cdc8 |
|---|---|
| 1 <tool id="bowtie_genomic_wrapper" name="Bowtie Genome Alignment" version="1.6.0"> | 1 <tool id="bowtie_genomic_wrapper" name="Bowtie Genome Alignment" version="1.7.1"> |
| 2 <description>Align to the Genome with Bowtie</description> | 2 <description>Align to the Genome with 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 |
| 160 <option value="indexed">Use a built-in index</option> | 160 <option value="indexed">Use a built-in index</option> |
| 161 <option value="history">Use one from the history</option> | 161 <option value="history">Use one from the history</option> |
| 162 </param> | 162 </param> |
| 163 <when value="indexed"> | 163 <when value="indexed"> |
| 164 <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> | 164 <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> |
| 165 <options from_data_table="bowtie_indexes"> | 165 <options from_data_table="bowtie_genome_refs2"> |
| 166 <filter type="sort_by" column="2" /> | 166 <filter type="sort_by" column="2" /> |
| 167 <validator type="no_options" message="No indexes are available" /> | 167 <validator type="no_options" message="No indexes are available" /> |
| 168 </options> | 168 </options> |
| 169 </param> | 169 </param> |
| 170 </when> | 170 </when> |
| 422 </conditional> <!-- singlePaired --> | 422 </conditional> <!-- singlePaired --> |
| 423 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" /> | 423 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" /> |
| 424 <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" /> | 424 <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 </inputs> | 425 </inputs> |
| 426 <outputs> | 426 <outputs> |
| 427 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> | 427 <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads"> |
| 428 <actions> | 428 <actions> |
| 429 <conditional name="refGenomeSource.genomeSource"> | 429 <conditional name="refGenomeSource.genomeSource"> |
| 430 <when value="indexed"> | 430 <when value="indexed"> |
| 431 <action type="metadata" name="dbkey"> | 431 <action type="metadata" name="dbkey"> |
| 432 <option type="from_data_table" name="bowtie_indexes" column="1" offset="0"> | 432 <option type="from_data_table" name="bowtie_indexes" column="1" offset="0"> |