diff Users/oconnorlab/Desktop/agile/agile_wrapper.xml @ 0:d6a426afaa46 default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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+++ b/Users/oconnorlab/Desktop/agile/agile_wrapper.xml	Tue Jun 07 16:22:51 2011 -0400
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+<tool id="agile_wrapper" name="AGILE" version="1.0.0">
+  <description> Quickly match reads to a reference genome or sequence file</description>
+  <command interpreter="python">
+    #if $source.source_select=="database" #agile_wrapper.py 0 $source.dbkey $input_query $output1 $max_sims $tile_size $max_freq $out_type $all
+    #else                                 #agile_wrapper.py 1 $source.input_target $input_query $output1 $max_sims $tile_size $max_freq $out_type $all
+    #end if# ${GALAXY_DATA_INDEX_DIR}
+  </command>
+	<inputs>
+	<conditional name="source">
+		<param name="source_select" type="select" label="Target source">
+				<option value="database">Genome Build</option>
+				<option value="input_ref">Your Upload File</option>
+		</param>
+		<when value="database">
+			<param name="dbkey" type="genomebuild" label="Genome" />
+		</when>
+		<when value="input_ref">
+			<param name="input_target" type="data" label="Reference sequence" />
+ 		</when>
+	</conditional>	
+		<param name="input_query" type="data" format="fasta" label="Query sequences file"/>
+		<param name="max_sims" type="integer" size="15" value="7" label="Maximum number of Single Imperfect Matches (SIMs) allowed as percentage of read length (-maxSIMs, default 7)" />
+		<param name="tile_size" type="integer" size="15" value="20" label="Sets the length of tuples for creating hash table (-tileSize, default 20)" help="Usually between 11 and 20."/>
+		<param name="max_freq" type="integer" size="15" value="8" label="Maximum number of occurrences of a pattern (k-tupple) allowed (-maxFreq, default 8"/>
+		<param name="all" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output all matches? (-all, default true for MHC)"/>
+		<param name="out_type" type="select" label="Output Format (-out default pslx for MHC">
+				<option value="pslx">pslx</option>
+				<option value="psl">psl</option>
+				<option value="axt">axt</option>
+				<option value="maf">maf</option>
+				<option value="sim4">sim4</option>
+				<option value="wublast">wublast</option>				
+				<option value="blast">blast</option>
+				<option value="blast8">blast8</option>
+				<option value="blast9">blast9</option>
+		</param>
+	</inputs>
+	<outputs>
+		<data name="output1" format="tabular"/>
+	</outputs>
+	<requirements>
+	    <requirement type="binary">agile</requirement>
+	</requirements>
+	<help>
+	
+.. class:: warningmark 
+
+The default parameter values can be altered in the agile tool xml file
+
+-----
+	
+**What it does**
+ 
+This tool uses the **AGILE** alignment program, a faster replacement for the **BLAT** algorithm. Your reads file is searched against a genome build or another uploaded file. 
+
+-----
+
+**Parameters**
+
+- *Maximum Single Imperfect Matches* (**-maxSIMs**) : The number of allowable mismatches as a percentage of read length.
+
+- *Tuple Length* (**-tileSize**) : The length of tuples for craring a hash table.
+
+- *Maximum Frequency* (**-maxFreq**) : The maximum number of pattern occurrences allowed.
+
+- *All Matches* (**-all**) : Output all matches satisfying the match criteria (true/false).
+
+- *Output Format* (**-out**) : Define the output format for the match file.
+
+-----
+
+**Reference**
+ 
+ **AGILE**: Sanchit Misra, Ankit Agrawal, Wei-keng Liao, Alok Choudhary. Anatomy of a Hash-based Long Read Sequence Mapping Algorithm for Next Generation DNA Sequencing. Bioinformatics 2010; doi: 10.1093/bioinformatics/btq648.
+
+
+	</help>
+</tool>