--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mira3.xml	Fri Aug 23 00:30:33 2019 -0400
@@ -0,0 +1,281 @@
+<tool id="mira3" name="MIRA Assembler v3" version="3.4.1.1">
+
+    <description>Assemble short/long/hybrid reads using MIRA 3.4</description>
+
+    <!-- ***************************************************************** -->
+
+    <requirements>
+        <requirement type="package" version="3.4.1.1">mira</requirement>
+    </requirements>
+
+    <!-- ***************************************************************** -->
+
+    <version_command>mira --version | perl -wnE'print "$1\n" for /This is MIRA V([\d\.]+)/g'</version_command>
+
+    <!-- ***************************************************************** -->
+
+    <command detect_errors="aggressive">
+    <![CDATA[
+
+    mira
+    --project=mira
+    --job=$job_method,$job_type,$job_quality
+    -GE:not="\${GALAXY_SLOTS:-1}"
+    #if $condBackbone.use == "true":
+        ## Can this be linked to job_method as well? If mapping we need the backbone...
+        -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
+    #end if
+    #if $condSanger.use == "true":
+        SANGER_SETTINGS
+        ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
+        ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+        -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
+        ${condSanger.sanger_extra}
+    #end if
+    #if $condRoche.use == "true":
+        454_SETTINGS
+        ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
+        ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+        -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
+        ${condRoche.roche_extra}
+    #end if
+    #if $condIllumina.use == "true":
+        SOLEXA_SETTINGS
+        ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
+        -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
+        ${condIllumina.solexa_extra}
+        ##TODO - Look at -LR FASTQ qual offset (fqqo)
+    #end if
+    #if $condIonTorrent.use == "true":
+        IONTOR_SETTINGS
+        ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
+        ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+        -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
+        ${condIonTorrent.torrent_extra}
+    #end if
+
+    COMMON_SETTINGS
+    $common_extra
+
+    ##ignore warnings about long read names
+    -MI:somrnl=0
+
+    ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
+    ##Explicitly disable formats we won't use like MAF (reduce IO)
+    -OUT:orf=$output_fasta:orc=$output_caf:ora=$output_ace:orw=$output_wig:orm=0:org=0:ors=0
+
+    ##remove_rollover_tmps, remove_tmp_directory
+    -OUT:rrot=1:rtd=1
+
+    ##put mira temp directory on local storage                                                                              
+    ##NO, must run from NFS or problems with multiple jobs/same name can arise
+    ##-DI:trt=/tmp
+    -MI:sonfs=no
+    ]]>
+    </command>
+
+    <!-- ***************************************************************** -->
+
+    <inputs>
+        <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
+            <option value="denovo">De novo</option>
+            <option value="mapping">Mapping</option>
+        </param>
+        <param name="job_type" type="select" label="Assembly type">
+            <option value="genome">Genome</option>
+            <option value="est">EST (transcriptome)</option>
+        </param>
+        <param name="job_quality" type="select" label="Assembly quality grade">
+            <option value="accurate">Accurate</option>
+            <option value="normal">Normal (deprecated)</option>
+            <option value="draft">Draft</option>
+        </param>
+        <!-- Backbone -->
+        <conditional name="condBackbone">
+            <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
+                <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
+            </when>
+        </conditional>
+        <!-- Sanger -->
+        <conditional name="condSanger">
+            <param name="use" type="select" label="Sanger/Capillary reads?">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
+                <param name="sanger_extra" type="text" size="100" value="" label="extra Sanger parameters for MIRA">
+                    <sanitizer invalid_char="">
+                        <valid initial=",string.letters,string.digits">
+                            <add value=" " />
+                            <add value="-" />
+                            <add value=":" />
+                            <add value="=" />
+                        </valid>
+                    </sanitizer>
+                </param>
+            </when>
+        </conditional>
+        <!-- Roche 454 -->
+        <conditional name="condRoche">
+            <param name="use" type="select" label="454 reads?">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
+                <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
+                <param name="roche_extra" type="text" size="100" value="" label="extra 454 parameters for MIRA">
+                    <sanitizer invalid_char="">
+                        <valid initial=",string.letters,string.digits">
+                            <add value=" " />
+                            <add value="-" />
+                            <add value=":" />
+                            <add value="=" />
+                        </valid>
+                    </sanitizer>
+                </param>
+            </when>
+        </conditional>
+        <!-- Illumina -->
+        <conditional name="condIllumina">
+            <param name="use" type="select" label="Solexa/Illumina reads?">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
+                <param name="solexa_extra" type="text" size="100" value="-DP:ure=yes -AS:mrpc=100 -AL:mo=16" label="extra Illumina parameters for MIRA">
+                    <sanitizer invalid_char="">
+                        <valid initial=",string.letters,string.digits">
+                            <add value=" " />
+                            <add value="-" />
+                            <add value=":" />
+                            <add value="=" />
+                        </valid>
+                    </sanitizer>
+                </param>
+            </when>
+        </conditional>
+        <!-- Ion Torrent -->
+        <conditional name="condIonTorrent">
+            <param name="use" type="select" label="Ion Torrent reads?">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
+                <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
+                <param name="torrent_extra" type="text" size="100" value="" label="extra IonTorrent parameters for MIRA">
+                    <sanitizer invalid_char="">
+                        <valid initial=",string.letters,string.digits">
+                            <add value=" " />
+                            <add value="-" />
+                            <add value=":" />
+                            <add value="=" />
+                        </valid>
+                    </sanitizer>
+                </param>
+            </when>
+        </conditional>
+        <param name="common_extra" type="text" size="100" value="-CO:mr=yes:mroir=no:asir=yes -SK:mnr=no:mmhr=.2 -AS:urd=no:ard=no:sd=yes:sdlpo=no" label="extra common parameters for MIRA">
+            <sanitizer invalid_char="">
+                <valid initial=",string.letters,string.digits">
+                    <add value=" " />
+                    <add value="-" />
+                    <add value=":" />
+                    <add value="=" />
+                </valid>
+            </sanitizer>
+        </param>
+	    <param name="output_fasta" type="boolean" truevalue="1" falsevalue="0" checked="yes" label="Output FASTA" />
+	    <param name="output_caf" type="boolean" truevalue="1" falsevalue="0" checked="0" label="Output CAF" />
+	    <param name="output_ace" type="boolean" truevalue="1" falsevalue="0" checked="0" label="Output ACE" />
+	    <param name="output_wig" type="boolean" truevalue="1" falsevalue="0" checked="0" label="Output WIG" />
+    </inputs>
+
+    <!-- ***************************************************************** -->
+
+    <outputs>
+        <data name="out_log" format="txt" label="MIRA log" from_work_dir="mira_assembly/mira_d_info/mira_info_assembly.txt" />
+        <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" from_work_dir="mira_assembly/mira_d_results/mira_out.unpadded.fasta">
+            <filter>output_fasta is True</filter>
+        </data>
+        <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" from_work_dir="mira_assembly/mira_d_results/mira_out.unpadded.fasta.qual">
+            <filter>output_fasta is True</filter>
+        </data>
+        <data name="out_caf" format="txt" label="MIRA contigs (CAF)" from_work_dir="mira_assembly/mira_d_results/mira_out.caf" >
+            <filter>output_caf is True</filter>
+        </data>
+        <data name="out_ace" format="txt" label="MIRA contigs (ACE)" from_work_dir="mira_assembly/mira_d_results/mira_out.ace">
+            <filter>output_ace is True</filter>
+        </data>
+        <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" from_work_dir="mira_assembly/mira_d_results/mira_out.wig">
+            <filter>output_wig is True</filter>
+        </data>
+    </outputs>
+
+    <!-- ***************************************************************** -->
+
+    <tests>
+        <test>
+            <param name="job_method" value="denovo" />
+            <param name="job_type" value="est" />
+            <param name="job_qual" value="accurate" />
+            <param name="condBackbone|use" value="false" />
+            <param name="condSanger|use" value="true" />
+            <param name="condSanger|filename" value="tvc_mini.fastq" ftype="fastq" />
+            <param name="condRoche|use" value="false" />
+            <param name="condIllumina|use" value="false" />
+            <param name="condIonTorrent|use" value="false" />
+            <param name="output_fasta" value="true" />
+            <param name="output_caf" value="false" />
+            <param name="output_ace" value="false" />
+            <param name="output_wig" value="false" />
+            <param name="common_extra" value="" />
+            <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
+        </test>
+    </tests>
+
+    <!-- ***************************************************************** -->
+
+    <help>
+
+**What it does**
+
+Runs MIRA v3.4, collects the output, and throws away all the temporary files.
+
+MIRA is an open source assembly tool capable of handling sequence data from
+a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also
+Ion Torrent).
+
+It is particularly suited to small genomes such as bacteria.
+
+    </help>
+
+    <!-- ***************************************************************** -->
+
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="bibtex">@ARTICLE{Chevreux1999-mira3,
+        author = {B. Chevreux and T. Wetter and S. Suhai},
+        year = {1999},
+        title = {Genome Sequence Assembly Using Trace Signals and Additional Sequence Information},
+        journal = {Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB)}
+        volume = {99},
+        pages = {45-56},
+        url = {http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html}
+        }</citation>
+    </citations>
+
+</tool>