diff barcode_splitter-bc23f6946bb8/fastx_barcode_splitter.xml @ 0:2b6d577dd1ab default tip

Uploaded

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+++ b/barcode_splitter-bc23f6946bb8/fastx_barcode_splitter.xml	Mon Jan 16 22:38:10 2012 -0500
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+<tool id="cshl_fastx_barcode_splitter" name="Barcode Splitter" force_history_refresh="True">
+	<description></description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
+	<command interpreter="python">fastx_barcode_splitter_galaxy_wrapper.py 
+           ## params for galaxy wrapper
+           $output 
+           "$output.id" 
+           "$input.ext" 
+           "$__new_file_path__" 
+           --barcodes='$barcodes'
+           $BARCODE $input "$input.name" "$output.extra_files_path" 
+           ## params for fastx_barcode_splitter
+            --mismatches $mismatches --partial $partial $EOL 
+        </command>
+
+	<inputs>
+		<param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
+                <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
+
+		<param name="EOL" type="select" label="Barcodes found at">
+			<option value="--bol">Start of sequence (5' end)</option>
+			<option value="--eol">End of sequence (3' end)</option>
+		</param>
+
+		<param name="mismatches" type="integer" size="3" value="2" label="Number of allowed mismatches" />
+		
+		<param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
+
+                <param name="barcodes" type="select" multiple="true" label="Select barcodes to add as new datasets to history">
+		    <options from_dataset="BARCODE">
+    			<column name="name" index="0"/>
+    			<column name="value" index="0"/>
+                        <filter type="unique_value" name="unq_bc" column="0" />
+                        <filter type="add_value" name="unmatched" value="unmatched"/>
+		    </options>
+                </param>
+	</inputs>
+
+	<outputs>
+		<data format="html" name="output" />
+	</outputs>
+	
+	<tests>
+		<test>
+			<!-- Split a FASTQ file -->
+			<param name="BARCODE" value="fastx_barcode_splitter1.txt" />
+			<param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
+			<param name="EOL" value="Start of sequence (5' end)" />
+			<param name="mismatches" value="2" />
+			<param name="partial" value="0" />
+			<output name="output" file="fastx_barcode_splitter1.out" />
+		</test>
+	</tests>
+
+<help>
+
+**What it does**
+
+This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria.
+
+--------
+
+**Barcode file Format**
+
+Barcode files are simple text files.
+Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character.
+Example::
+
+    #This line is a comment (starts with a 'number' sign)
+    BC1	GATCT
+    BC2	ATCGT
+    BC3	GTGAT
+    BC4 TGTCT
+    
+For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
+Sequences matching the barcode will be stored in the appropriate file.
+
+One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.
+
+The output of this tool is an HTML file, displaying the split counts and the file locations.
+
+**Output Example**
+
+.. image:: ./static/fastx_icons/barcode_splitter_output_example.png
+
+</help>
+</tool>
+<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon ([e-mail]) -->