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Remove no longer supported ROD datatypes from GATK tools (version 1.3).

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This commit is contained in:
Daniel Blankenberg
2011-11-21 16:41:19 -05:00
parent 8986dc2c81
commit d5f735faac
2 changed files with 12 additions and 12 deletions
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tools/gatk/indel_realigner.xml
+4 -4
View File
@@ -147,17 +147,17 @@
<option value="custom">Custom</option>
</param>
<when value="dbsnp">
<param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
<param name="input_rod" type="data" format="vcf" label="ROD file" />
</when>
<when value="snps">
<param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
<param name="input_rod" type="data" format="vcf" label="ROD file" />
</when>
<when value="indels">
<param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
<param name="input_rod" type="data" format="vcf" label="ROD file" />
</when>
<when value="custom">
<param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
<param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
<param name="input_rod" type="data" format="vcf" label="ROD file" />
</when>
</conditional>
</repeat>
tools/gatk/variant_recalibrator.xml
+8 -8
View File
@@ -179,7 +179,7 @@
<option value="custom">Custom</option>
</param>
<when value="variant">
<param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="Variant ROD file" />
<param name="input_rod" type="data" format="vcf" label="Variant ROD file" />
<conditional name="rod_training_type">
<param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
<option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -198,7 +198,7 @@
</conditional>
</when>
<when value="comp">
<param name="input_rod" type="data" format="vcf,gatk_dbsnp" label="ROD file" />
<param name="input_rod" type="data" format="vcf" label="ROD file" />
<param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/>
<conditional name="rod_training_type">
<param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
@@ -218,7 +218,7 @@
</conditional>
</when>
<when value="dbsnp">
<param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
<param name="input_rod" type="data" format="vcf" label="ROD file" />
<conditional name="rod_training_type">
<param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
<option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -237,7 +237,7 @@
</conditional>
</when>
<when value="snps">
<param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
<param name="input_rod" type="data" format="vcf" label="ROD file" />
<conditional name="rod_training_type">
<param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
<option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -256,7 +256,7 @@
</conditional>
</when>
<when value="hapmap">
<param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
<param name="input_rod" type="data" format="vcf" label="ROD file" />
<conditional name="rod_training_type">
<param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
<option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -275,7 +275,7 @@
</conditional>
</when>
<when value="omni">
<param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
<param name="input_rod" type="data" format="vcf" label="ROD file" />
<conditional name="rod_training_type">
<param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
<option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -294,7 +294,7 @@
</conditional>
</when>
<when value="indels">
<param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
<param name="input_rod" type="data" format="vcf" label="ROD file" />
<conditional name="rod_training_type">
<param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
<option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -314,7 +314,7 @@
</when>
<when value="custom">
<param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
<param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
<param name="input_rod" type="data" format="vcf" label="ROD file" />
<conditional name="rod_training_type">
<param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
<option value="is_training_truth_known">Set training/truth/known sites</option>