diff racon.xml @ 0:51fd3136069d draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/racon.xml	Mon Jun 11 16:47:50 2018 -0400
@@ -0,0 +1,81 @@
+<tool id="racon" name="Racon" version="1.3.1">
+    <description>Consensus module for raw de novo DNA assembly of long uncorrected reads.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <version_command>racon --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$reads' reads.${reads.ext} && 
+        ln -s '$overlaps' overlaps.${overlaps.ext} && 
+        ln -s '$corrected_reads' corrected_reads.${corrected_reads.ext} && 
+
+        racon 
+            reads.${reads.ext}  
+            overlaps.${overlaps.ext}  
+            corrected_reads.${corrected_reads.ext}
+            -t \${GALAXY_SLOTS:-4} 
+            $u
+            $f
+            -w $w
+            -q $q
+            -e $e
+            -m $m
+            -x $x
+            -g $g
+            > racon_polished_consensus.fa  
+    ]]></command>
+    <inputs>
+        <param type="data" name="reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Sequences"/>
+        <param type="data" name="overlaps" format="sam" label="Overlaps"/>
+        <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/>
+
+        <param argument="-u" type="boolean" truevalue="-u" falsevalue="" label="output unpolished target sequences" />
+        <param argument="-f" type="boolean" truevalue="-f" falsevalue="" label="perform fragment correction instead of contig polishing" />
+        <param argument="-w" type="integer" value="500" label="Size of window on which POA is performed" />
+        <param argument="-q" type="float" value="10.0" label="Threshold for average base quality of windows used in poa" />
+        <param argument="-e" type="float" value="0.3" label="Maximum allowed error rate used for filtering overlaps" />
+        <param argument="-m" type="integer" value="5" label="Score for matching bases" />
+        <param argument="-x" type="integer" value="-4" label="Score for mismatching bases" />
+        <param argument="-g" type="integer" value="-8" max="0" label="Gap penalty" />        
+        
+    </inputs>
+    <outputs>
+        <data name="consensus" format="fasta" from_work_dir="racon_polished_consensus.fa" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
+            <param name="overlaps" ftype="sam" value="sample_overlaps.sam"/>
+            <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
+            <param name="u" value="true"/>
+            <param name="f" value="true"/>
+            <param name="w" value="800"/>
+            <param name="e" value="0.2"/>
+            <output name="consensus" ftype="fasta" file="consensus_result2.fasta"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+Consensus module for raw de novo DNA assembly of long uncorrected reads.
+
+Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods
+which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar
+or better quality compared to the output generated by assembly methods which employ both error correction
+and consensus steps, while providing a speedup of several times compared to those methods.
+It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.
+
+Racon can be used as a polishing tool after the assembly with either Illumina data or data
+produced by third generation of sequencing. The type of data inputed is automatically detected.
+
+Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ
+format and overlaps/alignments between the reads and the contigs in SAM format. Output is a set of polished contigs in FASTA format printed to stdout.
+
+Racon can also be used as a read error-correction tool. In this scenario, the SAM file needs
+to contain pairwise overlaps between reads including dual overlaps.
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>