Mercurial > repos > peterjc > seq_filter_by_id
diff tools/seq_filter_by_id/seq_filter_by_id.xml @ 6:03e134cae41a draft
v0.2.3, ignore blank lines in ID file (contributed by Gildas Le Corguille)
| author | peterjc |
|---|---|
| date | Tue, 17 May 2016 05:59:24 -0400 |
| parents | 832c1fd57852 |
| children | fb1313d79396 |
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--- a/tools/seq_filter_by_id/seq_filter_by_id.xml Wed May 13 11:03:57 2015 -0400 +++ b/tools/seq_filter_by_id/seq_filter_by_id.xml Tue May 17 05:59:24 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.2"> +<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.3"> <description>from a tabular file</description> <requirements> <requirement type="package" version="1.64">biopython</requirement> @@ -12,17 +12,17 @@ <version_command interpreter="python">seq_filter_by_id.py --version</version_command> <command interpreter="python"> seq_filter_by_id.py -i "$input_file" -f "$input_file.ext" -#if $output_choice_cond.output_choice=="both" - -p $output_pos -n $output_neg -#elif $output_choice_cond.output_choice=="pos" - -p $output_pos -#elif $output_choice_cond.output_choice=="neg" - -n $output_neg +#if str($output_choice_cond.output_choice)=="both" + -p "$output_pos" -n "$output_neg" +#elif str($output_choice_cond.output_choice)=="pos" + -p "$output_pos" +#elif str($output_choice_cond.output_choice)=="neg" + -n "$output_neg" #end if -#if $adv_opts.adv_opts_selector=="advanced" and $adv_opts.strip_suffix +#if str($adv_opts.adv_opts_selector)=="advanced" and $adv_opts.strip_suffix -s #end if -#if $id_opts.id_opts_selector=="tabular": +#if str($id_opts.id_opts_selector)=="tabular": ## TODO - Decide on best way to expose multiple ID files via the XML wrapper. ## Single tabular file, can call the Python script with either UNION or INTERSECTION -l UNION "$id_opts.input_tabular" "$id_opts.columns"