comparison bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml @ 20:d93f47e97f98 draft

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author jackcurragh
date Fri, 10 Feb 2023 10:07:34 +0000
parents 75f8e498d26f
children 494b4d7145a9
comparison
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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>