Mercurial > repos > peterjc > seq_filter_by_id

comparison tools/filters/seq_filter_by_id.xml @ 2:abdd608c869b draft

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Uploaded v0.0.5, checked script return code for errors X copes with a FASTA entry missing an ID.
author peterjc
date Wed, 24 Apr 2013 11:34:12 -0400
parents 262f08104540
children
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1:262f08104540 2:abdd608c869b
1 <tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.0.4"> 1 <tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.0.5">
2 <description>from a tabular file</description> 2 <description>from a tabular file</description>
3 <version_command interpreter="python">seq_filter_by_id.py --version</version_command> 3 <version_command interpreter="python">seq_filter_by_id.py --version</version_command>
4 <command interpreter="python"> 4 <command interpreter="python">
5 seq_filter_by_id.py $input_tabular $columns $input_file $input_file.ext 5 seq_filter_by_id.py $input_tabular $columns $input_file $input_file.ext
6 #if $output_choice_cond.output_choice=="both" 6 #if $output_choice_cond.output_choice=="both"
9 $output_pos - 9 $output_pos -
10 #elif $output_choice_cond.output_choice=="neg" 10 #elif $output_choice_cond.output_choice=="neg"
11 - $output_neg 11 - $output_neg
12 #end if 12 #end if
13 </command> 13 </command>
14 <stdio>
15 <!-- Anything other than zero is an error -->
16 <exit_code range="1:" />
17 <exit_code range=":-1" />
18 </stdio>
14 <inputs> 19 <inputs>
15 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to filter on the identifiers" help="FASTA, FASTQ, or SFF format." /> 20 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to filter on the identifiers" help="FASTA, FASTQ, or SFF format." />
16 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> 21 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
17 <param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" label="Column(s) containing sequence identifiers" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"> 22 <param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" label="Column(s) containing sequence identifiers" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
18 <validator type="no_options" message="Pick at least one column"/> 23 <validator type="no_options" message="Pick at least one column"/>