Mercurial > repos > jackcurragh > ribogalaxy_bowtie_transcriptome

comparison bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml @ 10:5f3a3790cc79 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jackcurragh
date Sat, 20 Aug 2022 11:38:55 +0000
parents 15e6eb67d710
children edc0f39f80db
comparison
equal deleted inserted replaced
9:15e6eb67d710 10:5f3a3790cc79
1 <tool id="bowtie_transcriptomic_wrapper" name="Bowtie Transcriptome Alignment" version="1.4.0"> 1 <tool id="bowtie_transcriptomic_wrapper" name="Bowtie Transcriptome Alignment" version="1.5.0">
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
220 <param name="sPaired" type="select" label="Is this library mate-paired?"> 220 <param name="sPaired" type="select" label="Is this library mate-paired?">
221 <option value="single">Single-end</option> 221 <option value="single">Single-end</option>
222 <option value="paired">Paired-end</option> 222 <option value="paired">Paired-end</option>
223 </param> 223 </param>
224 <when value="single"> 224 <when value="single">
225 <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/> 225 <param name="sInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
226 <conditional name="sParams"> 226 <conditional name="sParams">
227 <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> 227 <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
228 <option value="preSet">Commonly used</option> 228 <option value="preSet">Commonly used</option>
229 <option value="full" selected="true">Full parameter list</option> 229 <option value="full" selected="true">Full parameter list</option>
230 </param> 230 </param>
312 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> 312 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
313 </when> <!-- full --> 313 </when> <!-- full -->
314 </conditional> <!-- sParams --> 314 </conditional> <!-- sParams -->
315 </when> <!-- single --> 315 </when> <!-- single -->
316 <when value="paired"> 316 <when value="paired">
317 <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> 317 <param name="pInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
318 <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"> 318 <param name="pInput2" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
319 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()"> 319 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
320 <column name="name" index="0"/> 320 <column name="name" index="0"/>
321 <column name="value" index="0"/> 321 <column name="value" index="0"/>
322 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/> 322 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>
323 </options> 323 </options>