Mercurial > repos > avowinkel > gatk
view generation/gatk.xsl @ 0:b80ff7f43ad1 draft default tip
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
author | avowinkel |
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date | Thu, 24 Sep 2015 12:10:01 -0400 |
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<?xml version="1.0" encoding="UTF-8"?> <xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"> <xsl:output method="xml" encoding="utf-8" indent="yes" cdata-section-elements="script style" /> <xsl:template match="/"> <tool id="gatk" name="GATK" version="@VERSION@.d9"> <description>tool collection Version @VERSION@</description> <macros> <import>gatk_macros.xml</import> <xsl:for-each select="analyses/analysis"> <import><xsl:value-of select="macro_file" /></import> </xsl:for-each> </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> <xsl:text disable-output-escaping="yes"><![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 ]]></xsl:text> </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"> <!--filter type="data_meta" key="dbkey" ref="@TAG@_input" column="dbkey" /--> </options> <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"> <xsl:for-each select="analyses/analysis"> <option value="{name}"><xsl:value-of select="name" /></option> </xsl:for-each> </param> <xsl:for-each select="analyses/analysis"> <when value="{name}"> <!--xsl:choose> <xsl:when test="input_type = 'bam'"> <expand macro="macro_bam_input" tag="{tag}" /> </xsl:when> <xsl:when test="input_type = 'gvcf'"> <expand macro="macro_gvcf_input" tag="{tag}" /> </xsl:when> </xsl:choose--> <expand macro="{name}Parameters" tag="{tag}" /> </when> </xsl:for-each> </conditional> </inputs> <outputs> <xsl:for-each select="analyses/analysis"> <expand macro="{name}Output" tag="{tag}"> <filter>analysis_type['analysis_type_selector'] == '<xsl:value-of select="name" />'</filter> </expand> </xsl:for-each> <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> </xsl:template> </xsl:stylesheet>