--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira4/mira4_convert.xml	Fri Nov 21 06:42:56 2014 -0500
@@ -0,0 +1,114 @@
+<tool id="mira_4_0_convert" name="MIRA v4.0 miraconvert" version="0.0.5">
+    <description>Convert MIRA assembly to FASTA/SAM/BAM</description>
+    <requirements>
+        <requirement type="binary">miraconvert</requirement>
+        <requirement type="package" version="4.0">MIRA</requirement>
+    </requirements>
+    <version_command interpreter="python">mira4_convert.py --version</version_command>
+    <command interpreter="python">
+mira4_convert.py
+--input "$mira_file"
+--min_length $min_length
+--min_cover $min_cover
+--min_reads $min_reads
+#if str($maf_wanted)=="true":
+--maf "$out_maf"
+#end if
+#if str($fasta_wanted)=="true":
+--fasta "$out_fasta"
+#end if
+#if str($bam_wanted)=="true":
+--bam "$out_bam"
+#end if
+##Don't yet have a Galaxy datatype defined for ace:
+## #if str($ace_wanted)=="true":
+## --ace "$out_ace"
+## #end if
+#if str($cstats_wanted)=="true":
+--cstats "$out_cstats"
+#end if
+    </command>
+    <stdio>
+        <!-- Assume anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <inputs>
+        <param name="mira_file" type="data" format="mira" required="true" label="MIRA Assembly Format input" />
+        <!-- TODO - top level select for contig versus read output? Or two Galaxy tools in different XML files? -->
+        <param name="min_length" type="integer" required="false" value="0" min="0"
+               label="Minimum contig length"
+               help="e.g. Set to 1000 to exclude small contigs. Default is to keep all contigs (minimum zero)" />
+        <param name="min_cover" type="integer" required="false" value="0" min="0"
+               label="Minimum average contig coverage"
+               help="e.g. Set to 10 to exclude low coverage contigs. Default is to keep all contigs (minimum zero)" />
+        <param name="min_reads" type="integer" required="false" value="0" min="0"
+               label="Minimum reads per contig"
+               help="e.g. Set to 5 to exclude low coverage contigs with only a few reads. Default is to keep all contigs (minimum zero)." />
+        <param name="maf_wanted" type="boolean" label="Output assembly in MIRA's own format? (useful if filtering)" checked="False" />
+        <param name="fasta_wanted" type="boolean" label="Convert assembly into (unpadded) FASTA?" checked="True" />
+        <param name="bam_wanted" type="boolean" label="Convert assembly into (upadded) BAM format?" checked="False" />
+        <!-- Don't yet have a Galaxy datatype defined for ace:
+        <param name="ace_wanted" type="boolean" label="Convert assembly in ACE format?" checked="False" />
+        -->
+        <param name="cstats_wanted" type="boolean" label="Assembly statistics file?" checked="False" />
+    </inputs>
+    <outputs>
+        <data name="out_maf" format="mira" label="$mira_file.name (filtered)">
+              <filter>maf_wanted is True</filter>
+        </data>
+        <data name="out_fasta" format="fasta" label="$mira_file.name (as FASTA)">
+              <filter>fasta_wanted is True</filter>
+        </data>
+        <data name="out_bam" format="bam" label="$mira_file.name (as BAM)">
+              <filter>bam_wanted is True</filter>
+        </data>
+        <!--
+        <data name="out_ace" format="ace" label="$mira_file.name (as ACE)">
+            <filter>ace_wanted is True</filter>
+        </data>
+        -->
+        <data name="out_cstats" format="tabular" label="$mira_file.name (filtered stats)">
+              <filter>cstats_wanted is True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- TODO -->
+    </tests>
+    <help>
+**What it does**
+
+Runs the ``miraconvert`` utility from MIRA v4.0 to filter and/or convert
+a MIRA Assembly Format file produced by a *mapping* or *de novo* assembly.
+
+**Example Usage**
+
+You want to remove all the low coverage contigs from a transcriptome
+assembly to focus on those with higher coverage.
+
+You want to convert your MIRA assembly into SAM/BAM to run a standard
+SNP finding tool.
+
+You've lost the FASTA consensus from your MIRA assembly and need to
+regenerate it.
+
+
+**Citation**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
+Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
+Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
+http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
+
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
+    </help>
+</tool>