opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-25 00:12:08 +08:00
Code Issues Packages Projects Releases Wiki Activity

Add no_options validator to built-in reference genome selector in GATK tools.

Browse Source
This commit is contained in:
Daniel Blankenberg
2011-11-30 13:29:21 -05:00
parent 6a90bd29f6
commit ceaa71e4e8
13 changed files with 13 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files
tools/gatk/count_covariates.xml
+1
View File
@@ -146,6 +146,7 @@
<options from_data_table="gatk_picard_indexes">
<filter type="data_meta" key="dbkey" ref="input_bam" 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>
</when>
<when value="history"> <!-- FIX ME!!!! -->
tools/gatk/depth_of_coverage.xml
+1
View File
@@ -194,6 +194,7 @@
<options from_data_table="gatk_picard_indexes">
<!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
</options>
<validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
</param>
</when>
<when value="history"> <!-- FIX ME!!!! -->
tools/gatk/indel_realigner.xml
+1
View File
@@ -124,6 +124,7 @@
<options from_data_table="gatk_picard_indexes">
<filter type="data_meta" key="dbkey" ref="input_bam" 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>
</when>
<when value="history"> <!-- FIX ME!!!! -->
tools/gatk/realigner_target_creator.xml
+1
View File
@@ -112,6 +112,7 @@
<options from_data_table="gatk_picard_indexes">
<filter type="data_meta" key="dbkey" ref="input_bam" 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>
</when>
<when value="history">
tools/gatk/table_recalibration.xml
+1
View File
@@ -129,6 +129,7 @@
<options from_data_table="gatk_picard_indexes">
<filter type="data_meta" key="dbkey" ref="input_bam" 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>
</when>
<when value="history"> <!-- FIX ME!!!! -->
tools/gatk/unified_genotyper.xml
+1
View File
@@ -154,6 +154,7 @@
<options from_data_table="gatk_picard_indexes">
<!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
</options>
<validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
</param>
</when>
<when value="history"> <!-- FIX ME!!!! -->
tools/gatk/variant_annotator.xml
+1
View File
@@ -157,6 +157,7 @@
<options from_data_table="gatk_picard_indexes">
<filter type="data_meta" key="dbkey" ref="input_variant" 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>
</when>
<when value="history"> <!-- FIX ME!!!! -->
tools/gatk/variant_apply_recalibration.xml
+1
View File
@@ -109,6 +109,7 @@
<options from_data_table="gatk_picard_indexes">
<!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" 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>
</when>
<when value="history"> <!-- FIX ME!!!! -->
tools/gatk/variant_combine.xml
+1
View File
@@ -121,6 +121,7 @@
<options from_data_table="gatk_picard_indexes">
<!-- <filter type="data_meta" key="dbkey" ref="input_variants.input_variant" 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>
</when>
<when value="history"> <!-- FIX ME!!!! -->
tools/gatk/variant_eval.xml
+1
View File
@@ -160,6 +160,7 @@
<options from_data_table="gatk_picard_indexes">
<!-- <filter type="data_meta" key="dbkey" ref="input_variant" 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>
</when>
<when value="history"> <!-- FIX ME!!!! -->
tools/gatk/variant_filtration.xml
+1
View File
@@ -110,6 +110,7 @@
<options from_data_table="gatk_picard_indexes">
<filter type="data_meta" key="dbkey" ref="input_variant" 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>
</when>
<when value="history"> <!-- FIX ME!!!! -->
tools/gatk/variant_recalibrator.xml
+1
View File
@@ -156,6 +156,7 @@
<options from_data_table="gatk_picard_indexes">
<!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" 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>
</when>
<when value="history"> <!-- FIX ME!!!! -->
tools/gatk/variants_validate.xml
+1
View File
@@ -96,6 +96,7 @@
<options from_data_table="gatk_picard_indexes">
<filter type="data_meta" key="dbkey" ref="input_variant" 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>
</when>
<when value="history"> <!-- FIX ME!!!! -->