| Previous changeset 2:18f459744a97 (2017-11-09) Next changeset 4:7ca6716748c2 (2018-12-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d |
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modified:
gemini_macros.xml gemini_query.xml |
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| diff -r 18f459744a97 -r 666f60a9331a gemini_macros.xml --- a/gemini_macros.xml Thu Nov 09 13:17:45 2017 -0500 +++ b/gemini_macros.xml Wed Oct 17 13:30:51 2018 -0400 |
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| @@ -88,14 +88,28 @@ <xml name="sanitize_query"> <sanitizer invalid_char=""> - <valid initial="string.printable"/> + <valid initial="string.printable"> + <remove value="'" /> + </valid> + <mapping initial="none"> + <add source="'" target="'"'"'" /> + </mapping> </sanitizer> </xml> + <token name="@MULTILN_SQL_EXPR_TO_CMDLN@"> + #set $sql_expr = str($multiline_sql_expr).strip() + #if str($sql_expr): + #set $sql_expr = $sql_expr.replace('\r\n', '\n') + #set $sql_expr = $sql_expr.replace('\r', '\n') + #set $sql_expr = $sql_expr.replace('\\\n', ' ') + $cmdln_param '$sql_expr' + #end if + </token> + <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@"> #if str($filter.filter_selector) == 'yes' and $filter.filter: - #import pipes - --filter ${ pipes.quote( str( $filter.filter ) ) or "''" } + --filter '${ str( $filter.filter ) }' #end if </token> |
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| diff -r 18f459744a97 -r 666f60a9331a gemini_query.xml --- a/gemini_query.xml Thu Nov 09 13:17:45 2017 -0500 +++ b/gemini_query.xml Wed Oct 17 13:30:51 2018 -0400 |
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| @@ -13,13 +13,13 @@ --in "${in}" - #if $gt_filter.strip(): - --gt-filter "${gt_filter}" - #end if + #set $multiline_sql_expr = $gt_filter + #set $cmdln_param = "--gt-filter" + @MULTILN_SQL_EXPR_TO_CMDLN@ - #if $sample_filter.strip(): - --sample-filter "${sample_filter}" - #end if + #set $multiline_sql_expr = $sample_filter + #set $cmdln_param = "--sample-filter" + @MULTILN_SQL_EXPR_TO_CMDLN@ $show_samples $show_families @@ -35,9 +35,9 @@ ##--format FORMAT Format of output (JSON, TPED or default) # we will take default for the time being ## --sample-delim STRING The delimiter to be used with the --show-samples option. - #if $q.strip(): - -q "${q}" - #end if + #set $multiline_sql_expr = $q + #set $cmdln_param = "-q" + @MULTILN_SQL_EXPR_TO_CMDLN@ "${ infile }" > "${ outfile }" |