comparison tools/filters/seq_select_by_id.xml @ 3:19e26966ed3e draft

Uploaded v0.0.6, handles Biopython dependency via the ToolShed, adopted MIT license, using reStructuredTest for the README file. No functional changes.

2:28d52478ace9

<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.4">
	<description>from a tabular file</description>
	<version_command interpreter="python">seq_select_by_id.py --version</version_command>
	<command interpreter="python">
seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file
	</command>
	<inputs>
		<param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." />
		<param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
		<param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/>
	</inputs>

Cock et al 2009. Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

	</help>
</tool>

3:19e26966ed3e

<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.6">
	<description>from a tabular file</description>
	<version_command interpreter="python">seq_select_by_id.py --version</version_command>
	<command interpreter="python">
seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file
	</command>
        <stdio>
                <!-- Anything other than zero is an error -->
                <exit_code range="1:" />
                <exit_code range=":-1" />
        </stdio>
	<inputs>
		<param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." />
		<param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
		<param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/>
	</inputs>

Cock et al 2009. Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

This tool is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
	</help>
</tool>