diff tools/mira4/mira4_de_novo.xml @ 0:32f693f6e741 draft

Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira4/mira4_de_novo.xml	Thu Sep 26 12:23:42 2013 -0400
@@ -0,0 +1,121 @@
+<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.1">
+    <description>Takes Sanger, Roche, Illumina, Ion Torrent and PacBio data</description>
+    <requirements>
+        <requirement type="python-module">Bio</requirement>
+        <requirement type="binary">mira</requirement>
+        <requirement type="package" version="4.0">MIRA</requirement>
+    </requirements>
+    <version_command interpreter="python">mira4.py -v</version_command>
+    <command interpreter="python">
+mira4.py $manifest $out_maf $out_fasta $out_log
+    </command>
+    <inputs>
+        <param name="job_type" type="select" label="Assembly type">
+            <option value="genome">Genome</option>
+            <option value="est">EST (transcriptome)</option>
+        </param>
+        <param name="job_quality" type="select" label="Assembly quality grade">
+            <option value="accurate">Accurate</option>
+            <option value="draft">Draft</option>
+        </param>
+        <repeat name="read_group" title="Read Group" min="1">
+            <param name="technology" type="select" label="Read technology" help="MIRA has different error models for different technologies">
+                <option value="solexa">Solexa/Illumina</option>
+                <option value="sanger">Sanger cappillary sequencing</option>
+                <option value="454">Roche 454</option>
+                <option value="iontor">Ion Torrent</option>
+                <option value="pcbiolq">PacBio low quality (raw)</option>
+                <option value="pcbiohq">PacBio high quality (corrected)</option>
+                <option value="text">Synthetic reads (database entries, consensus sequences, artifical reads, etc)</option>
+		<!-- TODO reference/backbone as an entry here? -->
+            </param>
+	    <repeat name="reads" title="Reads" min="1" help="Paired reads can be combined into one file, or given as two files. MIRA will look at the read names to identify pairs.">
+                <param name="filename" type="data" format="fastq" label="Reads in FASTQ format" />
+            </repeat>
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
+        <data name="out_maf" format="mira" label="MIRA Assembly" />
+        <data name="out_log" format="txt" label="MIRA log" />
+    </outputs>
+    <configfiles>
+        <configfile name="manifest">
+project = MIRA
+job = denovo,${job_type},${job_quality}
+parameters = -GE:not=1 -NW:cmrnl -DI:trt=/tmp
+## -GE:not is short for -GENERAL:number_of_threads and using one (1)
+## can be useful for repeatability of assemblies and bug hunting.
+##
+## -NW:cmrnl is short for -NAG_AND_WARN:check_maxreadnamelength
+## and without this MIRA aborts with read names over 40 characters
+## due to limitations of some downstream tools.
+##
+## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should
+## point to a local hard drive (not something like NFS on network).
+
+#for $rg in $read_group
+#=======================================================
+readgroup
+technology = ${rg.technology}
+##MIRA will accept multiple filenames on one data line, or multiple data lines
+#for f in $rg.reads
+data = ${f.filename}
+#end for
+### Cheetah doesn't want dollar sign on list comprehension intermediate variables
+###set $files = ' '.join([str(f['filename']) for f in rg['reads']])
+##data = $files
+#end for
+        </configfile>
+    </configfiles>
+    <tests>
+            <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
+                 strain data and miraSearchESTSNPs. Here we just assemble it. --> 
+<!--
+Commenting out test until Galaxy framework is fixed,
+https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-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" />
+            <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
+	</test>
+-->
+    </tests>
+    <help>
+
+**What it does**
+
+Runs MIRA v4.0 in de novo mode, 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, Ion Torrent
+and also PacBio).
+
+It is particularly suited to small genomes such as bacteria.
+
+**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>