--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira4_9/mirabait/mira4_9_mirabait.xml	Wed Oct 07 10:31:49 2015 -0400
@@ -0,0 +1,242 @@
+<tool id="mira4_9_mirabait" name="MIRA v4.9 mirabait" version="0.0.1">
+    <description>Filter reads using kmer matches</description>
+    <requirements>
+        <requirement type="binary">mirabait</requirement>
+        <requirement type="package" version="4.9.5">MIRA</requirement>
+    </requirements>
+    <stdio>
+        <!-- Assume anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <version_command interpreter="python">mira_check_version.py ${MIRA4_9}mirabait</version_command>
+    <command interpreter="python">./mira_check_version.py \${MIRA4_9}mirabait 4.9 &amp;&amp;
+##First checked it is mirabait v4.9 on the path... now actually run it
+##-----------------------------------------------------------------------
+\${MIRA4_9}mirabait -k "$kmer_length" -n "$min_occurence" -b "$bait_file"
+##-----------------------------------------------------------------------
+##Must now map Galaxy datatypes to MIRA file types...
+##exploiting the polymorphic naming of the input read parameter!
+#if $reads.filename.ext.startswith("fastq")
+##MIRA doesn't like fastqsanger etc, just plain old fastq
+ -f fastq -t fastq
+#elif $reads.filename.ext == "mira"
+##We're calling *.maf the "mira" format in Galaxy (name space collision)
+ -f maf -t maf
+#else
+##MIRA is happy with fasta as name,
+ -f "$reads.filename.ext" -t "$reads.filename.ext"
+#end if
+##-----------------------------------------------------------------------
+#if str($output_choice_cond.output_choice)=="both"
+-o "$output_pos" -O "$output_neg"
+#elif str($output_choice_cond.output_choice)=="pos"
+-o "$output_pos"
+#elif str($output_choice_cond.output_choice)=="neg"
+-i -O "$output_neg"
+#end if
+##-----------------------------------------------------------------------
+##Do we need to ignore the reverse strand?
+#if str($strand_choice) == "fwd"
+-r
+#end if
+##-----------------------------------------------------------------------
+##Default is to mark k-mers with upper case...
+#if str($output_case) == "original"
+-c
+#end if
+##-----------------------------------------------------------------------
+#if str($reads.type) == "paired"
+#if $reads.filename.ext != $reads.filename2.ext
+##TODO: Is there a better way to signal an error to Galaxy here?
+; echo "ERROR: Paired read datatype mis-match!" ; false
+#end if
+-p "$reads.filename" "$reads.filename2"
+#elif str($reads.type) == "interleaved"
+-P "$reads.filename"
+#elif str($reads.type) == "none"
+"$reads.filename"
+#end if
+    </command>
+    <inputs>
+        <!-- TODO: mirabait now allows multiple input files, and can do multiple outputs - or merge into one? -->
+        <!-- TODO: define a new Galaxy datatype for the bait hash file? -->
+        <param name="bait_file" type="data" format="fasta,fastq,mira" required="true" label="Bait file (what to look for)" />
+        <conditional name="reads">
+            <param name="type" type="select" label="Are these paired reads?">
+                <option value="paired">Paired reads (as two files)</option>
+                <option value="interleaved">Paired reads (as one interleaved file)</option>
+                <option value="none">Unpaired reads (single or orphan reads as one file)</option>
+            </param>
+            <when value="paired">
+                <param name="filename" type="data" format="fastq,fasta" required="true" label="Read file one"/>
+                <param name="filename2" type="data" format="fastq,fasta" required="true" label="Read file two"/>
+            </when>
+            <when value="interleaved">
+                <param name="filename" type="data" format="fasta,fastq" required="true" label="Interleaved paired reads to search" />
+            </when>
+            <when value="none">
+                <param name="filename" type="data" format="fasta,fastq,mira" required="true" label="Reads to search" />
+            </when>
+        </conditional>
+        <conditional name="output_choice_cond">
+            <param name="output_choice" type="select" label="Output positive matches, negative matches, or both?">
+                <option value="both">Both positive matches and negative matches, as two files</option>
+                <option value="pos" selected="true">Just positive matches, as a single file</option>
+                <option value="neg">Just negative matches, as a single file</option>
+            </param>
+            <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml -->
+            <when value="both" />
+            <when value="pos" />
+            <when value="neg" />
+        </conditional>
+        <param name="output_case" type="select" label="How to use sequence case in output?">
+            <option value="original">Preserve case from input</option>
+            <option value="bait">Mark k-mer matches in upper case</option>
+        </param>
+        <param name="strand_choice" type="select" label="Check for matches on both strands?">
+            <option value="both">Check both strands</option>
+            <option value="fwd">Just forward strand</option>
+        </param>
+        <param name="kmer_length" type="integer" value="31" min="1" max="256"
+               label="k-mer length" help="Maximum 256" />
+        <param name="min_occurence" type="integer" value="1" min="1"
+               label="Minimum k-mer occurence"
+               help="How many k-mer matches do you want per read? Minimum one" />
+    </inputs>
+    <outputs>
+        <data name="output_pos" format_source="filename" metadata_source="filename"
+             label="$reads.filename.name #if str($reads.type)=='paired' then 'and $reads.filename2.name' else ''# matching $bait_file.name">
+            <filter>output_choice_cond["output_choice"] != "neg"</filter>
+        </data>
+        <data name="output_neg" format_source="filename" metadata_source="filename"
+             label="$reads.filename.name #if str($reads.type)=='paired' then 'and $reads.filename2.name' else ''# not matching $bait_file.name">
+            <filter>output_choice_cond["output_choice"] != "pos"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
+            <param name="reads|type" value="none" />
+            <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" />
+            <param name="output_choice" value="pos" />
+            <param name="output_case" value="original" />
+            <output name="output_pos" file="tvc_mini_bait_pos.fastq" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
+            <param name="reads|type" value="none" />
+            <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" />
+            <param name="output_case" value="bait" />
+            <output name="output_pos" file="tvc_mini_bait_pos_case.fastq" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
+            <param name="reads|type" value="none" />
+            <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" />
+            <param name="output_case" value="bait" />
+            <output name="output_pos" file="tvc_mini_bait_pos_case.fastq" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
+            <param name="reads|type" value="none" />
+            <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" />
+            <param name="output_case" value="bait" />
+            <param name="kmer_length" value="32" />
+            <param name="min_occurence" value="50" />
+            <output name="output_pos" file="tvc_mini_bait_strict_case.fastq" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
+            <param name="reads|type" value="none" />
+            <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" />
+            <param name="output_choice" value="neg" />
+            <param name="output_case" value="original" />
+            <output name="output_neg" file="tvc_mini_bait_neg.fastq" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
+            <param name="reads|type" value="none" />
+            <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" />
+            <param name="output_choice" value="neg" />
+            <param name="output_case" value="bait" />
+            <output name="output_neg" file="tvc_mini_bait_neg_case.fastq" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
+            <param name="reads|type" value="none" />
+            <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" />
+            <param name="output_choice" value="both" />
+            <param name="output_case" value="original" />
+            <output name="output_pos" file="tvc_mini_bait_pos.fastq" ftype="fastqsanger" />
+            <output name="output_neg" file="tvc_mini_bait_neg.fastq" ftype="fastqsanger" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Runs the ``mirabait`` utility from MIRA v4.9 to filter your input reads
+according to whether or not they contain perfect kmer matches to your
+bait file. By default this looks for 31-mers (kmers or *k*-mers where
+the fragment length *k* is 31), and only requires a single matching kmer.
+
+The ``mirabait`` utility is useful in many applications and pipelines
+outside of using the main MIRA tool for assembly or mapping.
+
+.. class:: warningmark
+
+Note ``mirabait`` cannot be used on protein (amino acid) sequences.
+
+**Example Usage**
+
+To remove over abundant entries like rRNA sequences, run ``mirabait`` with
+known rRNA sequences as the bait and select the *negative* matches.
+
+To do targeted assembly by fishing out reads belonging to a gene and just
+assemble these, run ``mirabait`` with the gene of interest as the bait and
+select the *positive* matches.
+
+To iteratively reconstruct mitochondria you could start by fishing out reads
+matching any known mitochondrial sequence, assembly those, and repeat.
+
+
+**Notes on paired read**
+
+.. class:: warningmark
+
+Unlike ``mirabait`` from MIRA v4.0, this version is aware of paired reads
+and will preserve the pairing (if either the forward or the reverse read
+has enough *k*-mer matches, the pair is accepted).
+
+
+**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/mira_assembler_4_9
+    </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>