Mercurial > repos > peterjc > seq_filter_by_id

comparison tools/seq_filter_by_id/seq_filter_by_id.xml @ 6:03e134cae41a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
5:832c1fd57852 6:03e134cae41a
1 <tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.2"> 1 <tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.3">
2 <description>from a tabular file</description> 2 <description>from a tabular file</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.64">biopython</requirement> 4 <requirement type="package" version="1.64">biopython</requirement>
5 <requirement type="python-module">Bio</requirement> 5 <requirement type="python-module">Bio</requirement>
6 </requirements> 6 </requirements>
10 <exit_code range=":-1" /> 10 <exit_code range=":-1" />
11 </stdio> 11 </stdio>
12 <version_command interpreter="python">seq_filter_by_id.py --version</version_command> 12 <version_command interpreter="python">seq_filter_by_id.py --version</version_command>
13 <command interpreter="python"> 13 <command interpreter="python">
14 seq_filter_by_id.py -i "$input_file" -f "$input_file.ext" 14 seq_filter_by_id.py -i "$input_file" -f "$input_file.ext"
15 #if $output_choice_cond.output_choice=="both" 15 #if str($output_choice_cond.output_choice)=="both"
16 -p $output_pos -n $output_neg 16 -p "$output_pos" -n "$output_neg"
17 #elif $output_choice_cond.output_choice=="pos" 17 #elif str($output_choice_cond.output_choice)=="pos"
18 -p $output_pos 18 -p "$output_pos"
19 #elif $output_choice_cond.output_choice=="neg" 19 #elif str($output_choice_cond.output_choice)=="neg"
20 -n $output_neg 20 -n "$output_neg"
21 #end if 21 #end if
22 #if $adv_opts.adv_opts_selector=="advanced" and $adv_opts.strip_suffix 22 #if str($adv_opts.adv_opts_selector)=="advanced" and $adv_opts.strip_suffix
23 -s 23 -s
24 #end if 24 #end if
25 #if $id_opts.id_opts_selector=="tabular": 25 #if str($id_opts.id_opts_selector)=="tabular":
26 ## TODO - Decide on best way to expose multiple ID files via the XML wrapper. 26 ## TODO - Decide on best way to expose multiple ID files via the XML wrapper.
27 ## Single tabular file, can call the Python script with either UNION or INTERSECTION 27 ## Single tabular file, can call the Python script with either UNION or INTERSECTION
28 -l UNION "$id_opts.input_tabular" "$id_opts.columns" 28 -l UNION "$id_opts.input_tabular" "$id_opts.columns"
29 #else 29 #else
30 -t "$id_opts.id_list" 30 -t "$id_opts.id_list"