1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/1d1af17bbdcf/ changeset: 1d1af17bbdcf user: dan date: 2012-01-17 21:28:00 summary: Better handling of JEXL expressions in GATK. affected #: 2 files
diff -r 13535bd0c2c9d312bf44476c28b5eb916c5318a1 -r 1d1af17bbdcf9940a3a0cce62fe16d0189f9ad07 tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -1,4 +1,4 @@ -<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.4"> +<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.5"><description></description><requirements><requirement type="package" version="1.3">gatk</requirement> @@ -329,11 +329,12 @@ <when value="advanced"><repeat name="stratifications" title="Stratification"><param name="select_exps" value="" type="text" label="Stratification Expression"> - <sanitizer> - <valid> - <add value="""/> - </valid> - </sanitizer> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"/> + </sanitizer></param><param name="select_name" value="" type="text" label="Name"/></repeat>
diff -r 13535bd0c2c9d312bf44476c28b5eb916c5318a1 -r 1d1af17bbdcf9940a3a0cce62fe16d0189f9ad07 tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -1,9 +1,10 @@ -<tool id="gatk_variant_filtration" name="Variant Filtration" version="0.0.3"> +<tool id="gatk_variant_filtration" name="Variant Filtration" version="0.0.4"><description>on VCF files</description><requirements><requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py + #from binascii import hexlify --max_jvm_heap_fraction "1" --stdout "${output_log}" -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" @@ -17,12 +18,11 @@ #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" #end if + ' #for $variant_filter in $variant_filters: - --${variant_filter.is_genotype_filter}Expression "${variant_filter.filter_expression}" - --${variant_filter.is_genotype_filter}Name "${variant_filter.filter_name}" + #set $variant_filter = "--%sExpression '%s' --%sName '%s'" % ( str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_expression ), str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_name ) ) + -o '${ hexlify( $variant_filter ) }' #end for - ' -
#if str( $mask_rod_bind_type.mask_rod_bind_type_selector ) == 'set_mask': -d "--mask:${mask_rod_bind_type.mask_rod_name},%(file_type)s" "${mask_rod_bind_type.input_mask_rod}" "${mask_rod_bind_type.input_mask_rod.ext}" "input_mask_${mask_rod_bind_type.mask_rod_name}" @@ -125,7 +125,6 @@ <sanitizer><valid initial="string.printable"><remove value="'"/> - <remove value="""/></valid><mapping initial="none"/></sanitizer>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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