Mercurial > repos > jackcurragh > ribogalaxy_bowtie_transcriptome
comparison bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml @ 10:5f3a3790cc79 draft
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author | jackcurragh |
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date | Sat, 20 Aug 2022 11:38:55 +0000 |
parents | 15e6eb67d710 |
children | edc0f39f80db |
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9:15e6eb67d710 | 10:5f3a3790cc79 |
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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> |