diff realigner_target_creator.xml @ 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/realigner_target_creator.xml	Thu Sep 24 12:10:01 2015 -0400
@@ -0,0 +1,57 @@
+<macros>
+    <xml name="RealignerTargetCreatorParameters" tokens="tag">
+        
+        <expand macro="macro_bam_input" tag="@TAG@" />
+
+        <expand macro="macro_optional_parameters">
+            <param name="maxIntervalSize" type="integer" value="500" label="maximum interval size; any intervals larger than this value will be dropped" help="-maxInterval,&#8209;&#8209;maxIntervalSize &amp;lt;maxIntervalSize&amp;gt;" />
+            <param name="minReadsAtLocus" type="integer" value="4" label="minimum reads at a locus to enable using the entropy calculation" help="-minReads,&#8209;&#8209;minReadsAtLocus &amp;lt;minReadsAtLocus&amp;gt;" />
+            <param name="windowSize" type="integer" value="10" label="window size for calculating entropy or SNP clusters" help="-window,&#8209;&#8209;windowSize &amp;lt;windowSize&amp;gt;" />
+
+            <param name="mismatchFraction" type="float" value="0.0" label="fraction of base qualities needing to mismatch for a position to have high entropy" help="-mismatch,&#8209;&#8209;mismatchFraction &amp;lt;mismatchFraction&amp;gt;" />
+            <repeat name="rod_bindings" title="Input VCF files with known indels" help="-known,&#8209;&#8209;known &amp;lt;known&amp;gt;">
+                <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" />
+            </repeat>
+        </expand>
+        
+    </xml>
+
+    <xml name="RealignerTargetCreatorOutput">
+        <data format="gatk_interval" name="rtc_output_intervals" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (GATK intervals)">
+            <yield />
+        </data>
+    </xml>
+
+    <template name="RealignerTargetCreatorPreprocessing">
+<![CDATA[
+        @token_bam_input_pre@
+
+        #if $analysis_type.optional_parameters.optional_parameters_enabled
+            #for $i, $rod_binding in enumerate($analysis_type.optional_parameters.rod_bindings):
+                ln -s -f ${rod_binding.input_rod} rod_binding_${i}.vcf &&
+            #end for
+        #end if
+]]>
+    </template>
+
+    <template name="RealignerTargetCreatorOptions">
+<![CDATA[
+        --out                   ${rtc_output_intervals}
+
+        @token_bam_input@
+
+        #if $analysis_type.optional_parameters.optional_parameters_enabled
+            --maxIntervalSize       ${analysis_type.optional_parameters.maxIntervalSize}
+            --minReadsAtLocus       ${analysis_type.optional_parameters.minReadsAtLocus}
+            --windowSize            ${analysis_type.optional_parameters.windowSize}
+            --mismatchFraction      ${analysis_type.optional_parameters.mismatchFraction}
+
+            #for $i, $rod_binding in enumerate($analysis_type.optional_parameters.rod_bindings):
+                --known rod_binding_${i}.vcf
+            #end for
+        #end if
+]]>
+    </template>
+</macros>
+
+