diff tools/filters/seq_rename.xml @ 0:a4b9836f8f47

Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/seq_rename.xml	Tue Jun 07 17:43:26 2011 -0400
@@ -0,0 +1,56 @@
+<tool id="seq_rename" name="Rename sequences" version="0.0.1">
+	<description>with ID mapping from a tabular file</description>
+	<command interpreter="python">
+seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file
+	</command>
+	<inputs>
+		<param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." />
+		<param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
+		<param name="old_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing current (old) sequence identifiers"/>
+                <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column contai
+ning new sequence identifiers"/>
+	</inputs>
+	<outputs>
+		<data name="output_file" format="fasta" label="Renamed ${on_string}">
+			<!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
+			<change_format>
+				<when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
+				<when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
+				<when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
+				<when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
+				<when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
+				<when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
+			</change_format>
+		</data>
+	</outputs>
+	<tests>
+	</tests>
+	<requirements>
+		<requirement type="python-module">Bio</requirement>
+	</requirements>
+	<help>
+
+**What it does**
+
+Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a
+new sequence file (of the same format) where the sequence identifiers have been
+renamed according two the specified columns a the tabular file.
+
+WARNING: If you have any duplicates in the intput sequence file, you will still
+have duplicate sequences in the output.
+
+WARNING: If the tabular file has more than one new name for any old ID, the
+last one is used.
+
+**Citation**
+
+This tool uses Biopython to read and write SFF files. If you use this tool in
+scientific work leading to a publication, please cite the Biopython application
+note (and Galaxy too of course):
+
+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>