Mercurial > repos > sanbi-uwc > gatk2
changeset 1:25b1bbfe9d13 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit 4551dc00ae1447b86952c0c8e845496c264f3ccb
author | sanbi-uwc |
---|---|
date | Thu, 19 Apr 2018 08:25:49 -0400 |
parents | 6e985e2e0802 |
children | b1584795d565 |
files | unified_genotyper.xml variant_annotator.xml variant_recalibrator.xml |
diffstat | 3 files changed, 10 insertions(+), 10 deletions(-) [+] |
line wrap: on
line diff
--- a/unified_genotyper.xml Wed Jan 25 08:00:49 2017 -0500 +++ b/unified_genotyper.xml Thu Apr 19 08:25:49 2018 -0400 @@ -151,8 +151,8 @@ <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &lt;annotation&gt;"> <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> <options from_data_table="gatk2_annotations"> - <filter type="multiple_splitter" column="tools_valid_for" separator=","/> - <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> + <filter type="multiple_splitter" column="3" separator=","/> + <filter type="static_value" value="UnifiedGenotyper" column="3"/> </options> </param> <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &lt;annotation&gt;"> @@ -185,8 +185,8 @@ help="-XA,--excludeAnnotation &lt;excludeAnnotation&gt;" > <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> <options from_data_table="gatk2_annotations"> - <filter type="multiple_splitter" column="tools_valid_for" separator=","/> - <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> + <filter type="multiple_splitter" column="3" separator=","/> + <filter type="static_value" value="UnifiedGenotyper" column="3"/> </options> </param> <param name="sample_ploidy" type="integer" value="2"
--- a/variant_annotator.xml Wed Jan 25 08:00:49 2017 -0500 +++ b/variant_annotator.xml Thu Apr 19 08:25:49 2018 -0400 @@ -119,8 +119,8 @@ <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" help="-A,--annotation &lt;annotation&gt;" > <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> <options from_data_table="gatk2_annotations"> - <filter type="multiple_splitter" column="tools_valid_for" separator=","/> - <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/> + <filter type="multiple_splitter" column="3" separator=","/> + <filter type="static_value" value="VariantAnnotator" column="3"/> </options> </param> </when> @@ -173,8 +173,8 @@ <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &lt;excludeAnnotation&gt;" > <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> <options from_data_table="gatk2_annotations"> - <filter type="multiple_splitter" column="tools_valid_for" separator=","/> - <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/> + <filter type="multiple_splitter" column="3" separator=","/> + <filter type="static_value" value="VariantAnnotator" column="3"/> </options> </param>
--- a/variant_recalibrator.xml Wed Jan 25 08:00:49 2017 -0500 +++ b/variant_recalibrator.xml Thu Apr 19 08:25:49 2018 -0400 @@ -300,8 +300,8 @@ <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation &lt;use_annotation&gt;"> <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> <options from_data_table="gatk2_annotations"> - <filter type="multiple_splitter" column="tools_valid_for" separator=","/> - <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/> + <filter type="multiple_splitter" column="3" separator=","/> + <filter type="static_value" value="VariantRecalibrator" column="3"/> </options> </param>