Mercurial > repos > jackcurragh > ribogalaxy_bowtie_transcriptome
comparison bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml @ 20:d93f47e97f98 draft
Uploaded
| author | jackcurragh |
|---|---|
| date | Fri, 10 Feb 2023 10:07:34 +0000 |
| parents | 75f8e498d26f |
| children | 494b4d7145a9 |
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| 19:75f8e498d26f | 20:d93f47e97f98 |
|---|---|
| 1 <tool id="bowtie_trans_wrapper" name="Bowtie Transcriptome Alignment" version="1.7.5"> | 1 <tool id="bowtie_trans_wrapper" name="Bowtie Transcriptome Alignment" version="1.7.6"> |
| 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 |
| 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" help="if your reference of interest is not listed - contact RiboGalaxy team"> | 164 <param name="index" type="select" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team"> |
| 165 <options from_data_table="bowtie_transcriptome_indexes_3"> | 165 <options from_data_table="bowtie_transcriptome_indexes_4"> |
| 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> |
| 429 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> | 429 <data format="sam" name="output" label="${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_3" column="1" offset="0"> | 434 <option type="from_data_table" name="bowtie_transcriptome_indexes_4" column="1" offset="0"> |
| 435 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> | 435 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> |
| 436 <filter type="param_value" ref="refGenomeSource.index" column="0"/> | 436 <filter type="param_value" ref="refGenomeSource.index" column="0"/> |
| 437 </option> | 437 </option> |
| 438 </action> | 438 </action> |
| 439 </when> | 439 </when> |