Mercurial > repos > iuc > breseq
comparison breseq.xml @ 2:d515d94db821 draft
"planemo upload commit 9f3f6fbbe2653d4c42818a89d6897ddaef6706b1"
| author | iuc |
|---|---|
| date | Wed, 07 Apr 2021 12:17:17 +0000 |
| parents | 256cd7d32d15 |
| children | 58518ba76409 |
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| 1:256cd7d32d15 | 2:d515d94db821 |
|---|---|
| 5 <macros> | 5 <macros> |
| 6 <import>macros.xml</import> | 6 <import>macros.xml</import> |
| 7 </macros> | 7 </macros> |
| 8 | 8 |
| 9 <requirements> | 9 <requirements> |
| 10 <requirement type="package" version="0.34.0">breseq</requirement> | 10 <requirement type="package" version="0.35.5">breseq</requirement> |
| 11 <requirement type="package" version="1.32">tar</requirement> | 11 <requirement type="package" version="1.32">tar</requirement> |
| 12 </requirements> | 12 </requirements> |
| 13 | 13 |
| 14 <version_command>breseq --version</version_command> | 14 <version_command>breseq --version</version_command> |
| 15 | 15 |
| 128 <option value="annotate">Annotate</option> | 128 <option value="annotate">Annotate</option> |
| 129 <option value="compare">Compare</option> | 129 <option value="compare">Compare</option> |
| 130 </param> | 130 </param> |
| 131 <when value="detect"> | 131 <when value="detect"> |
| 132 | 132 |
| 133 <param name="fastqs" type="data" format="fastq" multiple="true" label="Fastq Read Files" /> | 133 <param name="fastqs" type="data" format="fastq,fastq.gz" multiple="true" label="Fastq Read Files" /> |
| 134 | 134 |
| 135 <param argument="--polymorphism-prediction" name="polymorphism_prediction" type="select" label="Detection Mode" help="**Polymorphism mode**: Detect variants with frequencies between 0% and 100% if a mixture model is well-supported by the read alignment evidence. Use to analyze a mixed population of genomes evolved from a common ancestor. **Consensus mode**: Detect variants present in 100% of the sample. Use when re-sequencing a clonal haploid genome. This mode is the default."> | 135 <param argument="--polymorphism-prediction" name="polymorphism_prediction" type="select" label="Detection Mode" help="**Polymorphism mode**: Detect variants with frequencies between 0% and 100% if a mixture model is well-supported by the read alignment evidence. Use to analyze a mixed population of genomes evolved from a common ancestor. **Consensus mode**: Detect variants present in 100% of the sample. Use when re-sequencing a clonal haploid genome. This mode is the default."> |
| 136 <option value="" selected="true">Consensus</option> | 136 <option value="" selected="true">Consensus</option> |
| 137 <option value="--polymorphism-prediction">Polymorphism</option> | 137 <option value="--polymorphism-prediction">Polymorphism</option> |
| 138 </param> | 138 </param> |
| 214 <param name="own_genome" value="lambda.gbk" /> | 214 <param name="own_genome" value="lambda.gbk" /> |
| 215 </conditional> | 215 </conditional> |
| 216 </repeat> | 216 </repeat> |
| 217 <conditional name="run"> | 217 <conditional name="run"> |
| 218 <param name="mode" value="detect" /> | 218 <param name="mode" value="detect" /> |
| 219 <param name="fastqs" value="lambda.short_sequence_repeats.fastq" /> | 219 <param name="fastqs" value="lambda.short_sequence_repeats.fastq.gz" ftype="fastq.gz" /> |
| 220 <param name="polymorphism_prediction" value="" /> | 220 <param name="polymorphism_prediction" value="" /> |
| 221 <param name="name" value="smallest" /> | 221 <param name="name" value="smallest" /> |
| 222 <param name="predict_junctions" value="" /> | 222 <param name="predict_junctions" value="" /> |
| 223 <section name="output_options"> | 223 <section name="output_options"> |
| 224 <param name="formats" value="html,log,gd,zip" /> | 224 <param name="formats" value="html,log,gd,zip" /> |
| 245 <param name="fixed_genome" value="lambda1" /> | 245 <param name="fixed_genome" value="lambda1" /> |
| 246 </conditional> | 246 </conditional> |
| 247 </repeat> | 247 </repeat> |
| 248 <conditional name="run"> | 248 <conditional name="run"> |
| 249 <param name="mode" value="detect" /> | 249 <param name="mode" value="detect" /> |
| 250 <param name="fastqs" value="lambda.short_sequence_repeats.fastq" /> | 250 <param name="fastqs" value="lambda.short_sequence_repeats.fastq.gz" ftype="fastq.gz"/> |
| 251 <param name="polymorphism_prediction" value="" /> | 251 <param name="polymorphism_prediction" value="" /> |
| 252 <param name="name" value="smallest" /> | 252 <param name="name" value="smallest" /> |
| 253 <param name="predict_junctions" value="" /> | 253 <param name="predict_junctions" value="" /> |
| 254 <section name="output_options"> | 254 <section name="output_options"> |
| 255 <param name="formats" value="gd" /> | 255 <param name="formats" value="gd" /> |