diff generation/gatk.xsl @ 0:b80ff7f43ad1 draft default tip

planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generation/gatk.xsl	Thu Sep 24 12:10:01 2015 -0400
@@ -0,0 +1,162 @@
+<?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">&lt;![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>&amp;1 | awk '\$1 != "INFO" &amp;&amp; \$1 != "WARN"' >&amp;2
+]]&gt;</xsl:text>
+    </command>
+
+    <inputs>
+
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,&#8209;&#8209;reference_sequence &amp;lt;reference_sequence&amp;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,&#8209;&#8209;intervals &amp;lt;intervals&amp;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,&#8209;&#8209;BQSR &amp;lt;BQSR&amp;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>
+
+