Mercurial > repos > iuc > gemini
changeset 4:ba3abde6775b draft default tip
Uploaded
| author | iuc |
|---|---|
| date | Thu, 15 Jan 2015 15:33:48 -0500 |
| parents | ed88ab9ead28 |
| children | |
| files | gemini_autosomal_recessive.xml gemini_comp_hets.xml gemini_de_novo.xml gemini_macros.xml gemini_region.xml tool_dependencies.xml |
| diffstat | 6 files changed, 15 insertions(+), 15 deletions(-) [+] |
line wrap: on
line diff
--- a/gemini_autosomal_recessive.xml Tue Jan 13 10:07:11 2015 -0500 +++ b/gemini_autosomal_recessive.xml Thu Jan 15 15:33:48 2015 -0500 @@ -21,9 +21,7 @@ --columns "${report.columns}" #end if - #if str($filter.filter_selector) == 'yes': - --filter "${filter.filter}" - #end if + @CMDLN_SQL_FILTER_FILTER_OPTION@ -d $d #if int($min_kindreds) > 0:
--- a/gemini_comp_hets.xml Tue Jan 13 10:07:11 2015 -0500 +++ b/gemini_comp_hets.xml Thu Jan 15 15:33:48 2015 -0500 @@ -14,9 +14,8 @@ --columns "${report.columns}" #end if - #if $filter.filter_selector == 'yes': - --filter "${filter.filter}" - #end if + @CMDLN_SQL_FILTER_FILTER_OPTION@ + $only_affected $ignore_phasing
--- a/gemini_de_novo.xml Tue Jan 13 10:07:11 2015 -0500 +++ b/gemini_de_novo.xml Thu Jan 15 15:33:48 2015 -0500 @@ -14,9 +14,8 @@ --columns "${report.columns}" #end if - #if $filter.filter_selector == 'yes': - --filter "${filter.filter}" - #end if + @CMDLN_SQL_FILTER_FILTER_OPTION@ + -d $d "${ infile }" > "${ outfile }"
--- a/gemini_macros.xml Tue Jan 13 10:07:11 2015 -0500 +++ b/gemini_macros.xml Thu Jan 15 15:33:48 2015 -0500 @@ -88,11 +88,17 @@ <xml name="sanitize_query"> <sanitizer invalid_char=""> - <valid initial="string.printable"> - </valid> + <valid initial="string.printable"/> </sanitizer> </xml> + <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@"> + #if str($filter.filter_selector) == 'yes' and $filter.filter: + #import pipes + --filter ${ pipes.quote( str( $filter.filter ) ) or "''" } + #end if + </token> + <xml name="min_sequence_depth"> <param name="d" type="integer" value="0" size="5" label="The minimum aligned sequence depth (genotype DP) required for each sample" help="default: 0 (-d)">
--- a/gemini_region.xml Tue Jan 13 10:07:11 2015 -0500 +++ b/gemini_region.xml Thu Jan 15 15:33:48 2015 -0500 @@ -24,9 +24,7 @@ --columns "${report.columns}" #end if - #if $filter.filter_selector == 'yes': - --filter "${filter.filter}" - #end if + @CMDLN_SQL_FILTER_FILTER_OPTION@ $header "${ infile }"
--- a/tool_dependencies.xml Tue Jan 13 10:07:11 2015 -0500 +++ b/tool_dependencies.xml Thu Jan 15 15:33:48 2015 -0500 @@ -13,6 +13,6 @@ <repository changeset_revision="fb3a854c7104" name="package_bedtools_2_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="gemini" version="0.10.0"> - <repository changeset_revision="42c72725f879" name="package_gemini_0_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="7c5b37efe4e5" name="package_gemini_0_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>