--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ribopicker.xml	Tue Oct 16 19:42:32 2012 -0400
@@ -0,0 +1,97 @@
+<tool id="ribopicker" name="riboPicker" version="1.0.0">
+    <description>Easy identification and removal of rRNA-like sequences.</description>
+    <version_command>ribopicker.pl -version | awk '{print $3}'</version_command>
+    <command interpreter="bash">ribopicker.sh
+        -id 'galaxy'
+    #if $identity_threshold:
+        -i $identity_threshold
+    #end if
+    #if $coverage_threshold:
+        -c $coverage_threshold
+    #end if
+    #if $length_threshold:
+        -l $length_threshold
+    #end if
+    #if $read_chunk_size:
+        -S $read_chunk_size
+    #end if
+    #if $z_best_value:
+        -z $z_best_value
+    #end if
+    #if $align_score_threshold:
+        -T $align_score_threshold
+    #end if
+     -f $input
+    </command>
+    <inputs>
+        <param name="input" type="data" format="fastq,fasta" label="from"
+            help="Input file in FASTA or FASTQ format that contains the query
+            sequences."/>
+        <param name="dbs" type="select" label="Reference Database">
+          <options from_data_table="ribopicker_dbs">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No reference databases are available" />
+          </options>
+        </param>
+    <param name="identity_threshold" type="integer" value="" size="3"
+        label="Alignment Identity Threshold" optional="True" help="Alignment
+        identity threshold in percentage (integer from 1-100 without %) used to
+        define matching sequences as similar. The identity is calculated for the
+        part of the query sequence that is aligned to a reference sequence. For
+        example, a query sequence of 100 bp that aligns to a reference sequence
+        over the first 50 bp with 40 matching positions has an identity value of
+        80%." >
+        <validator type="in_range" message="(1-100)" min="1" max="100"/>
+    </param>
+    <param name="coverage_threshold" type="integer" value="" size="3"
+        label="Alignment Coverage Threshold" optional="True" help="Alignment
+        coverage threshold in percentage (integer from 1-100 without %) used to
+        define matching sequences as similar. The coverage is calculated for the
+        part of the query sequence that is aligned to a reference sequence. For
+        example, a query sequence of 100 bp that aligns to a reference sequence
+        over the first 50 bp with 40 matching positions has an coverage value of
+        50%." >
+        <validator type="in_range" message="(1-100)" min="1" max="100"/>
+    </param>
+    <param name="length_threshold" type="integer" value="" size="5"
+        label="Alignment Length Threshold" optional="True" help="Alignment
+        length threshold used to define matching sequences as similar. For
+        example, a query sequence of 100 bp that aligns to a reference sequence
+        over the first 50 bp with 40 matching positions has an alignment length
+        of 50." >
+        <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
+    </param>
+    <param name="read_chunk_size" type="integer" value="" size="9"
+        label="Chunk size of reads in bp for BWA-SW" optional="True" help="Chunk
+        size of reads in bp as used by BWA-SW (default: 10000000)" >
+        <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
+    </param>
+    <param name="z_best_value" type="integer" value="" size="5"
+        label="Z-best value for BWA-SW" optional="True" help="Z-best value as
+        used by BWA-SW (default: 1)">
+        <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
+    </param>
+    <param name="align_score_threshold" type="integer" value="" size="5"
+        label="Alignment score threshold for BWA-SW" optional="True"
+        help="Alignment score threshold as used by BWA-SW (default: 30)" >
+        <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
+    </param>
+    </inputs>
+    <outputs>
+        <data name="rrna" format="fasta" from_work_dir="galaxy_rrna.txt" label="rRNA" />
+        <data name="nonrrna" format="fasta" from_work_dir="galaxy_nonrrna.txt" label="Non-rRNA" />
+    </outputs>
+    <!--
+    Usage:
+        ribopicker [options] -f <file> -dbs <list> ...
+    Options:
+        -T <integer>
+            Alignment score threshold as used by BWA-SW (default: 30).
+-->
+<help>
+**What it does**
+
+The riboPicker tool can be used to automatically identify and efficiently
+remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.
+</help>
+</tool>