Mercurial > repos > avowinkel > gatk
diff gatk.xml @ 0:b80ff7f43ad1 draft default tip
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
| author | avowinkel |
|---|---|
| date | Thu, 24 Sep 2015 12:10:01 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gatk.xml Thu Sep 24 12:10:01 2015 -0400 @@ -0,0 +1,179 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="gatk" name="GATK" version="@VERSION@.d9"> + <description>tool collection Version @VERSION@</description> + <macros> + <import>gatk_macros.xml</import> + <import>realigner_target_creator.xml</import> + <import>indel_realigner.xml</import> + <import>base_recalibrator.xml</import> + <import>analyze_covariates.xml</import> + <import>print_reads.xml</import> + <import>haplotype_caller.xml</import> + <import>genotype_gvcfs.xml</import> + <import>combine_gvcfs.xml</import> + <import>combine_variants.xml</import> + </macros> + <expand macro="requirements"/> + <stdio> + <regex match="^INFO" level="log"/> + <regex match="^WARN" level="warning"/> + <regex match="Using .* implementation of PairHMM" level="warning"/> + <regex match="There is insufficient memory for the Java Runtime Environment to continue" level="fatal"/> + <regex match="^##### ERROR" level="fatal"/> + <exit_code range="1:" level="fatal"/> + </stdio> + <command><![CDATA[ + ############################ + ## import analysis specific preprocessings by using cheetahs internal searchList + ## if not defined, ignore + ############################ + #if $analysis_type.analysis_type_selector + "Preprocessing" in vars()['SL'][2] + #set $analysisPreprocessing = vars()['SL'][2][$analysis_type.analysis_type_selector + "Preprocessing"] + #include source=$analysisPreprocessing + #end if + + ############################ + ## GATK tool unspecific options + ############################ + @GATK_EXEC@ + + --analysis_type ${analysis_type.analysis_type_selector} + --reference_sequence ${ref_file.fields.path} + + --log_to_file ${output_log} + + #if $cond_intervals.cond_intervals_enabled + #for $interval in $cond_intervals.intervals: + --intervals ${interval.L} + #end for + #end if + + #if $cond_BQSR.cond_BQSR_enabled + --BQSR $cond_BQSR.BQSR + #end if + + ############################ + ## import analysis specific options by using cheetahs internal searchList + ## if not defined throw raw python error until better idea + ############################ + #if $analysis_type.analysis_type_selector + "Options" in vars()['SL'][2] + #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"] + #include source=$analysisOptions + #else + #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"] + #end if + + ############################ + ## only put ERROR or FATAL log messages into stderr + ## but keep full log for printing into log file + ############################ + 2>&1 | awk '\$1 != "INFO" && \$1 != "WARN"' >&2 +]]></command> + <inputs> + <param name="ref_file" type="select" label="Using reference genome" help="-R,‑‑reference_sequence &lt;reference_sequence&gt;"> + <options from_data_table="picard_indexes"/> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + <conditional name="cond_intervals"> + <param name="cond_intervals_enabled" type="boolean" label="Select interval subset to operate on?"/> + <when value="true"> + <repeat name="intervals" title="genomic interval over which to operate" help="-L,‑‑intervals &lt;intervals&gt;"> + <param name="L" type="text" value=""/> + </repeat> + </when> + <when value="false"/> + </conditional> + <conditional name="cond_BQSR"> + <param name="cond_BQSR_enabled" type="boolean" label="Select covariates for on-the-fly recalibration?"/> + <when value="true"> + <param name="BQSR" type="data" format="tabular" label="Input covariates table file for on-the-fly base quality score recalibration" help="-BQSR,‑‑BQSR &lt;BQSR&gt; intended primarily for use with BaseRecalibrator and PrintReads"/> + </when> + <when value="false"/> + </conditional> + <conditional name="cond_threads"> + <param name="cond_threads_enabled" type="boolean" label="Set computational options (cpu, mem)?"/> + <when value="true"> + <param name="nt" type="integer" value="1" label="Number of data threads to allocate to this analysis" help="make sure, the option is available for the chosen tool"/> + <param name="nct" type="integer" value="1" label="Number of CPU threads to allocate per data thread" help="make sure, the option is available for the chosen tool"/> + <param name="mem" type="integer" value="0" label="Overwrite Memory in MB (0 = don't overwrite)" help="Overwrites all other defaults and might lead to crash the run. States mem per data thread"/> + </when> + <when value="false"/> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" type="select" label="Analysis Type"> + <option value="RealignerTargetCreator">RealignerTargetCreator</option> + <option value="IndelRealigner">IndelRealigner</option> + <option value="BaseRecalibrator">BaseRecalibrator</option> + <option value="AnalyzeCovariates">AnalyzeCovariates</option> + <option value="PrintReads">PrintReads</option> + <option value="HaplotypeCaller">HaplotypeCaller</option> + <option value="GenotypeGVCFs">GenotypeGVCFs</option> + <option value="CombineGVCFs">CombineGVCFs</option> + <option value="CombineVariants">CombineVariants</option> + </param> + <when value="RealignerTargetCreator"> + <expand macro="RealignerTargetCreatorParameters" tag="rtc"/> + </when> + <when value="IndelRealigner"> + <expand macro="IndelRealignerParameters" tag="ir"/> + </when> + <when value="BaseRecalibrator"> + <expand macro="BaseRecalibratorParameters" tag="br"/> + </when> + <when value="AnalyzeCovariates"> + <expand macro="AnalyzeCovariatesParameters" tag="ac"/> + </when> + <when value="PrintReads"> + <expand macro="PrintReadsParameters" tag="pr"/> + </when> + <when value="HaplotypeCaller"> + <expand macro="HaplotypeCallerParameters" tag="hc"/> + </when> + <when value="GenotypeGVCFs"> + <expand macro="GenotypeGVCFsParameters" tag="gg"/> + </when> + <when value="CombineGVCFs"> + <expand macro="CombineGVCFsParameters" tag="cg"/> + </when> + <when value="CombineVariants"> + <expand macro="CombineVariantsParameters" tag="cv"/> + </when> + </conditional> + </inputs> + <outputs> + <expand macro="RealignerTargetCreatorOutput" tag="rtc"> + <filter>analysis_type['analysis_type_selector'] == 'RealignerTargetCreator'</filter> + </expand> + <expand macro="IndelRealignerOutput" tag="ir"> + <filter>analysis_type['analysis_type_selector'] == 'IndelRealigner'</filter> + </expand> + <expand macro="BaseRecalibratorOutput" tag="br"> + <filter>analysis_type['analysis_type_selector'] == 'BaseRecalibrator'</filter> + </expand> + <expand macro="AnalyzeCovariatesOutput" tag="ac"> + <filter>analysis_type['analysis_type_selector'] == 'AnalyzeCovariates'</filter> + </expand> + <expand macro="PrintReadsOutput" tag="pr"> + <filter>analysis_type['analysis_type_selector'] == 'PrintReads'</filter> + </expand> + <expand macro="HaplotypeCallerOutput" tag="hc"> + <filter>analysis_type['analysis_type_selector'] == 'HaplotypeCaller'</filter> + </expand> + <expand macro="GenotypeGVCFsOutput" tag="gg"> + <filter>analysis_type['analysis_type_selector'] == 'GenotypeGVCFs'</filter> + </expand> + <expand macro="CombineGVCFsOutput" tag="cg"> + <filter>analysis_type['analysis_type_selector'] == 'CombineGVCFs'</filter> + </expand> + <expand macro="CombineVariantsOutput" tag="cv"> + <filter>analysis_type['analysis_type_selector'] == 'CombineVariants'</filter> + </expand> + <data format="txt" name="output_log" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (log)"/> + </outputs> + <expand macro="macro_tests"/> + <citations> + <citation type="doi">10.1101/gr.107524.110</citation> + <citation type="doi">10.1038/ng.806</citation> + <citation type="doi">10.1002/0471250953.bi1110s43</citation> + </citations> +</tool>