Mercurial > repos > peterjc > seq_filter_by_id

comparison tools/seq_filter_by_id/seq_filter_by_id.xml @ 9:141612f8c3e3 draft

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v0.2.7 Python 3 compatible print etc
author peterjc
date Thu, 11 May 2017 12:18:52 -0400
parents 2d4537dbf0bc
children 4a7d8ad2a983
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8:2d4537dbf0bc 9:141612f8c3e3
1 <tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.6"> 1 <tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.7">
2 <description>from a tabular file</description> 2 <description>from a tabular file</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.67">biopython</requirement> 4 <requirement type="package" version="1.67">biopython</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <version_command>
7 <!-- Anything other than zero is an error --> 7 python $__tool_directory__/seq_filter_by_id.py --version
8 <exit_code range="1:" /> 8 </version_command>
9 <exit_code range=":-1" /> 9 <command detect_errors="aggressive">
10 </stdio> 10 python $__tool_directory__/seq_filter_by_id.py -i '$input_file' -f '$input_file.ext'
11 <version_command interpreter="python">seq_filter_by_id.py --version</version_command>
12 <command interpreter="python">
13 seq_filter_by_id.py -i "$input_file" -f "$input_file.ext"
14 #if str($output_choice_cond.output_choice)=="both" 11 #if str($output_choice_cond.output_choice)=="both"
15 -p "$output_pos" -n "$output_neg" 12 -p '$output_pos' -n '$output_neg'
16 #elif str($output_choice_cond.output_choice)=="pos" 13 #elif str($output_choice_cond.output_choice)=="pos"
17 -p "$output_pos" 14 -p '$output_pos'
18 #elif str($output_choice_cond.output_choice)=="neg" 15 #elif str($output_choice_cond.output_choice)=="neg"
19 -n "$output_neg" 16 -n '$output_neg'
20 #end if 17 #end if
21 #if str($adv_opts.adv_opts_selector)=="advanced" and $adv_opts.strip_suffix 18 #if str($adv_opts.adv_opts_selector)=="advanced" and $adv_opts.strip_suffix
22 -s 19 -s
23 #end if 20 #end if
24 #if str($id_opts.id_opts_selector)=="tabular": 21 #if str($id_opts.id_opts_selector)=="tabular":
25 ## TODO - Decide on best way to expose multiple ID files via the XML wrapper. 22 ## TODO - Decide on best way to expose multiple ID files via the XML wrapper.
26 ## Single tabular file, can call the Python script with either UNION or INTERSECTION 23 ## Single tabular file, can call the Python script with either UNION or INTERSECTION
27 -l UNION "$id_opts.input_tabular" "$id_opts.columns" 24 -l UNION '$id_opts.input_tabular' '$id_opts.columns'
28 #else 25 #else
29 -t "$id_opts.id_list" 26 -t '$id_opts.id_list'
30 #end if 27 #end if
31 </command> 28 </command>
32 <inputs> 29 <inputs>
33 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to be filtered" help="FASTA, FASTQ, or SFF format." /> 30 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to be filtered" help="FASTA, FASTQ, or SFF format." />
34 <conditional name="id_opts"> 31 <conditional name="id_opts">