Mercurial > repos > devteam > freebayes
comparison freebayes.xml @ 11:e9ebed0c12f6 draft
Check exit code instead of stderr, since FreeBayes writes warnings there (e.g. "Could not find any mapped reads in target region chr1:955302..955952"). Also document change of available options in FreeBayes >= 0.9.9.
| author | soranzo |
|---|---|
| date | Mon, 17 Feb 2014 10:53:56 -0500 |
| parents | fcb60273c710 |
| children |
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| 10:07d55d9ea9a4 | 11:e9ebed0c12f6 |
|---|---|
| 154 #end if | 154 #end if |
| 155 ${options_type.section_algorithmic_features_type.use_mapping_quality} | 155 ${options_type.section_algorithmic_features_type.use_mapping_quality} |
| 156 --read-dependence-factor "${options_type.section_algorithmic_features_type.read_dependence_factor}" | 156 --read-dependence-factor "${options_type.section_algorithmic_features_type.read_dependence_factor}" |
| 157 ${options_type.section_algorithmic_features_type.no_marginals} | 157 ${options_type.section_algorithmic_features_type.no_marginals} |
| 158 #end if | 158 #end if |
| 159 | |
| 160 #end if | 159 #end if |
| 161 </command> | 160 </command> |
| 162 <inputs> | 161 <inputs> |
| 163 <conditional name="reference_source"> | 162 <conditional name="reference_source"> |
| 164 <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> | 163 <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> |
| 167 </param> | 166 </param> |
| 168 <when value="cached"> | 167 <when value="cached"> |
| 169 <repeat name="input_bams" title="Sample BAM file" min="1"> | 168 <repeat name="input_bams" title="Sample BAM file" min="1"> |
| 170 <param name="input_bam" type="data" format="bam" label="BAM file"> | 169 <param name="input_bam" type="data" format="bam" label="BAM file"> |
| 171 <validator type="unspecified_build" /> | 170 <validator type="unspecified_build" /> |
| 172 <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> | 171 <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> |
| 173 </param> | 172 </param> |
| 174 </repeat> | 173 </repeat> |
| 175 <param name="ref_file" type="select" label="Using reference genome"> | 174 <param name="ref_file" type="select" label="Using reference genome"> |
| 176 <options from_data_table="sam_fa_indexes"> | 175 <options from_data_table="sam_fa_indexes"> |
| 177 <!-- <filter type="sam_fa_indexes" key="dbkey" ref="input_bam" column="value"/> does not yet work in a repeat...--> | 176 <!-- <filter type="sam_fa_indexes" key="dbkey" ref="input_bam" column="value"/> does not yet work in a repeat...--> |
| 305 <param name="max_complex_gap" type="integer" label="Allow complex alleles with contiguous embedded matches of up to this length" value="" optional="True"/> | 304 <param name="max_complex_gap" type="integer" label="Allow complex alleles with contiguous embedded matches of up to this length" value="" optional="True"/> |
| 306 </when> | 305 </when> |
| 307 </conditional> | 306 </conditional> |
| 308 | 307 |
| 309 <!-- indel realignment --> | 308 <!-- indel realignment --> |
| 310 <param name="left_align_indels" type="boolean" truevalue="--left-align-indels" falsevalue="" checked="False" label="Left-realign and merge gaps embedded in reads" /> | 309 <!-- in FreeBayes < 0.9.9 the default is to not left-align indels and the available option is - -left-align-indels, |
| 310 in FreeBayes >= 0.9.9 the default is to left-align indels and the available option is - -dont-left-align-indels --> | |
| 311 <param name="left_align_indels" type="boolean" truevalue="--left-align-indels" falsevalue="" checked="False" label="Left align indels" /> | |
| 311 | 312 |
| 312 <!-- input filters --> | 313 <!-- input filters --> |
| 313 <conditional name="section_input_filters_type"> | 314 <conditional name="section_input_filters_type"> |
| 314 <param name="section_input_filters_type_selector" type="select" label="Set input filters options"> | 315 <param name="section_input_filters_type_selector" type="select" label="Set input filters options"> |
| 315 <option value="do_not_set" selected="True">Do not set</option> | 316 <option value="do_not_set" selected="True">Do not set</option> |
| 427 <param name="input_bam" ftype="bam" value="fake_phiX_reads_1.bam"/> | 428 <param name="input_bam" ftype="bam" value="fake_phiX_reads_1.bam"/> |
| 428 <param name="options_type_selector" value="basic"/> | 429 <param name="options_type_selector" value="basic"/> |
| 429 <output name="output_vcf" file="freebayes_out_1.vcf.contains" compare="contains"/> | 430 <output name="output_vcf" file="freebayes_out_1.vcf.contains" compare="contains"/> |
| 430 </test> | 431 </test> |
| 431 </tests> | 432 </tests> |
| 433 <stdio> | |
| 434 <exit_code range="1:" /> | |
| 435 </stdio> | |
| 432 <help> | 436 <help> |
| 433 **What it does** | 437 **What it does** |
| 434 | 438 |
| 435 This tool uses FreeBayes to call SNPS given a reference sequence and a BAM alignment file. | 439 This tool uses FreeBayes to call SNPS given a reference sequence and a BAM alignment file. |
| 436 | 440 |