--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spades.xml	Wed Dec 21 17:58:30 2016 -0500
@@ -0,0 +1,208 @@
+<tool id="spades" name="SPAdes" version="3.9.0">
+    <description>genome assembler for regular and single-cell projects</description>
+    <requirements>
+        <requirement type="package" version="3.9.0">spades</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command>
+    <![CDATA[
+    ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output
+    spades.py -o . --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16}
+    #if not $kmer_choice.auto_kmer_choice:
+        -k "$kmer_choice.kmers"
+    #end if
+    #if $cov.state == "auto":
+        --cov-cutoff 'auto'
+    #elif $cov.state == "value":
+        --cov-cutoff '$cov.cutoff'
+    #end if
+    $iontorrent
+    ## Sequence files, libraries
+    #for $i, $library in enumerate( $libraries, start=1 )
+        #if str( $library.lib_type ) == "paired_end":
+            #set prefix = 'pe'
+        #elif str( $library.lib_type ) == "mate_paired":
+            #set prefix = 'mp'
+        #elif str( $library.lib_type ) == "nxmate_paired":
+            #set prefix = 'nxmate'
+        #else:
+            #set prefix = 'hqmp'
+        #end if
+        --$prefix$i-$library.orientation
+        #for $file in $library.files
+            #if $file.file_type.type == "separate"
+                --$prefix$i-1 fastq:$file.file_type.fwd_reads
+                --$prefix$i-2 fastq:$file.file_type.rev_reads
+            #elif $file.file_type.type == "interleaved"
+                --$prefix$i-12 fastq:$file.file_type.interleaved_reads
+            #elif $file.file_type.type == "unpaired"
+                --$prefix$i-s fastq:$file.file_type.unpaired_reads
+            #elif $file.file_type.type == "paired-collection"
+                --$prefix$i-1 fastq:$file.file_type.fastq_collection.forward
+                --$prefix$i-2 fastq:$file.file_type.fastq_collection.reverse
+            #end if
+        #end for
+    #end for
+    #for $read in $pacbio_reads:
+        #if $read:
+            --pacbio fastq:$read
+        #end if
+    #end for
+    #for $read in $nanopore_reads:
+        #if $read:
+            --nanopore fastq:$read
+        #end if
+    #end for
+    #for $read in $sanger_reads:
+        #if $read:
+            --sanger $read.extension:$read
+        #end if
+    #end for
+    #for $contig in $trusted_contigs:
+        #if $contig:
+            --trusted-contigs $contig.extension:$contig
+        #end if
+    #end for
+    #for $contig in $untrusted_contigs:
+        #if $contig:
+            --untrusted-contigs $contig.extension:$contig
+        #end if
+    #end for
+    ]]>
+    </command>
+    <inputs>
+        <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean">
+            <option value="false">No</option>
+            <option value="true">Yes</option>
+        </param>
+        <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" />
+        <param argument="----careful" checked="True" falsevalue="" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector &#8211; a post processing tool, which uses BWA tool (comes with SPAdes)." label="Careful correction?" name="careful" truevalue="--careful" type="boolean" />
+        <conditional name="kmer_choice">
+            <param checked="False" falsevalue="false" help="k-mer choices can be chosen by SPAdes instead of being entered manually" label="Automatically choose k-mer values" name="auto_kmer_choice" truevalue="true" type="boolean" />
+            <when value="false">
+                <param help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." label="K-mers to use, separated by commas" name="kmers" type="text" value="21,33,55" />
+            </when>
+            <when value="true" />
+        </conditional>
+        <conditional name="cov">
+            <param label="Coverage Cutoff" name="state" type="select">
+                <option value="off">Off</option>
+                <option value="value">User Specific</option>
+                <option value="auto">Auto</option>
+            </param>
+            <when value="off" />
+            <when value="value">
+                <param help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" label="Coverage cutoff value" name="cutoff" type="float" value="" />
+            </when>
+            <when value="auto" />
+        </conditional>
+        <param checked="False" falsevalue="" label="Libraries are IonTorrent reads?" name="iontorrent" truevalue="--iontorrent" type="boolean" />
+        <repeat help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided." min="1" name="libraries" title="Libraries">
+            <param label="Library type" name="lib_type" type="select">
+                <option value="paired_end">Paired-end / Single reads</option>
+                <option value="mate_paired">Mate pairs</option>
+                <option value="high_mate_paired">High Quality Mate pairs</option>
+                <option value="nxmate_paired">Lucigen NxMate pairs</option>
+            </param>
+            <param label="Orientation" name="orientation" type="select">
+                <option selected="true" value="fr"><![CDATA[-> <- (fr)]]></option>
+                <option value="rf"><![CDATA[<- -> (rf)]]></option>
+                <option value="ff"><![CDATA[-> -> (ff)]]></option>
+            </param>
+            <repeat min="1" name="files" title="Files">
+                <conditional name="file_type">
+                    <param label="Select file format" name="type" type="select">
+                        <option value="separate">Separate input files</option>
+                        <option value="interleaved">Interleaved files</option>
+                        <option value="unpaired">Unpaired/Single reads</option>
+                        <option value="paired-collection">Paired List Collection</option>
+                    </param>
+                    <when value="separate">
+                        <param format="fastq" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" />
+                        <param format="fastq" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" />
+                    </when>
+                    <when value="interleaved">
+                        <param format="fastq" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" />
+                    </when>
+                    <when value="unpaired">
+                        <param format="fastq" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" />
+                    </when>
+                    <when value="paired-collection">
+                        <param collection_type="paired" format="fastq" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" />
+                    </when>
+                </conditional>
+            </repeat>
+        </repeat>
+        <param optional="true" format="fastq" label="PacBio CLR reads" multiple="true" name="pacbio_reads" type="data" />
+        <param optional="true" format="fastq" label="Nanopore reads" multiple="true" name="nanopore_reads" type="data" />
+        <param optional="true" format="fasta,fastq" label="Sanger reads" multiple="true" name="sanger_reads" type="data" />
+        <param optional="true" format="fasta,fastq" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" />
+        <param optional="true" format="fasta,fastq" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" />
+    </inputs>
+    <outputs>
+        <data format="fasta" from_work_dir="contigs.fasta" label="SPAdes contigs (fasta)" name="out_contigs" />
+        <data format="fasta" from_work_dir="scaffolds.fasta" label="SPAdes scaffolds (fasta)" name="out_scaffolds" />
+        <data format="txt" from_work_dir="spades.log" label="SPAdes log" name="out_log" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="sc" value="false" />
+            <param name="careful" value="false" />
+            <param name="kmers" value="33" />
+            <param name="lib_type" value="paired_end" />
+            <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
+            <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
+            <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
+        </test>
+        <test>
+            <param name="sc" value="false" />
+            <param name="careful" value="false" />
+            <param name="auto_kmer_choice" value="true" />
+            <param name="lib_type" value="paired_end" />
+            <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
+            <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
+            <output compare="re_match" file="auto_kmer_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
+        </test>
+        <test>
+            <param name="sc" value="false" />
+            <param name="careful" value="false" />
+            <param name="kmers" value="77" />
+            <param name="lib_type" value="paired_end" />
+            <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
+            <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
+            <output compare="re_match" file="kmer_77_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes.
+
+This wrapper runs SPAdes 3.9, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage.
+
+**License**
+
+SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
+
+This wrapper is copyrighted by Philip Mabon and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.
+
+** Acknowledgments **
+
+Original wrapper developed by Lionel Guy.
+
+Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
+
+Nicola Soranzo fixed various bugs.
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1089/cmb.2012.0021</citation>
+    </citations>
+</tool>