diff tools/mira4/mira4_de_novo.xml @ 6:626d5cfd01aa draft

Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)

--- a/tools/mira4/mira4_de_novo.xml	Tue Oct 15 12:07:34 2013 -0400
+++ b/tools/mira4/mira4_de_novo.xml	Mon Oct 21 12:01:47 2013 -0400
@@ -1,7 +1,6 @@
 <tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.1">
     <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
     <requirements>
-        <requirement type="python-module">Bio</requirement>
         <requirement type="binary">mira</requirement>
         <requirement type="package" version="4.0">MIRA</requirement>
     </requirements>
@@ -29,17 +28,39 @@
                 <option value="text">Synthetic reads (database entries, consensus sequences, artifical reads, etc)</option>
 		<!-- TODO reference/backbone as an entry here? -->
             </param>
-            <param name="segment_placement" type="select" label="Pairing type (segment placing)">
-                <option value="">None (e.g. single end sequencing)</option>
-                <option value="FR">---&gt; &lt;--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option>
-                <option value="RF">&lt;--- ---&gt; (e.g. Solexa/Illumina mate-pair library)</option>
-                <option value="SB">2---&gt; 1---&gt; (e.g. Roche 454 paired-end libraries or IonTorrent long-mate; see note)</option>
-                <option value="?">Unknown or not relevant (e.g. primer walking with Sanger capillary sequencing)</option>
-            </param>
+            <conditional name="segments">
+                <param name="type" type="select" label="Are these paired reads?">
+                    <option value="paired">Paired reads</option>
+                    <option value="none">Single reads or not relevant (e.g. primer walking with Sanger capillary sequencing)</option>
+                </param>
+                <when value="paired">
+                    <param name="placement" type="select" label="Pairing type (segment placing)">
+                        <option value="FR">---&gt; &lt;--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option>
+                        <option value="RF">&lt;--- ---&gt; (e.g. Solexa/Illumina mate-pair library)</option>
+                        <option value="SB">2---&gt; 1---&gt; (e.g. Roche 454 paired-end libraries or IonTorrent long-mate; see note)</option>
+                    </param>
+                    <!-- min/max validation is done via the <code> tag -->
+                    <param name="min_size" type="integer" optional="true" min="0" value=""
+                           label="Minimum size of 'good' DNA templates in the library preparation"
+                           help="Optional, but if used you must also supply a maximum value." /> 
+                    <param name="max_size" type="integer" optional="true" min="0" value=""
+                           label="Maximum size of 'good' DNA templates in the library preparation"
+                           help="Optional, but if used you must also supply a minimum value." />
+                    <param name="naming" type="select" label="Pair naming convention">
+                        <option value="solexa">Solexa/Illumina (using '/1' and '/2' suffixes)</option>
+                        <option value="FR">Forward/Reverse scheme (using '.f*' and '.r*' suffixes)</option>
+                        <option value="tigr">TIGR scheme (using 'TF*' and 'TR*' suffixes)</option>
+                        <option value="sanger">Sanger scheme (see notes)</option>
+                        <option value="stlouis">St. Louis scheme (see notes)</option>
+                    </param>
+                </when>
+                <when value="none" /><!-- no further questions -->
+            </conditional>
 	    <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)"
 		   help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
         </repeat>
     </inputs>
+    <code file="mira4_validator.py" />
     <outputs>
         <data name="out_fasta" format="fasta" label="MIRA de novo contigs (FASTA)" />
         <data name="out_maf" format="mira" label="MIRA de novo assembly" />
@@ -67,12 +88,20 @@
 
 readgroup
 technology = ${rg.technology}
+##Record the segment placement (if any)
+#if str($rg.segments.type) == "paired"
+segmentplacement = ${rg.segments.placement}
+segmentnaming = ${rg.segments.naming}
+#if str($rg.segments.min_size) != "" or str($rg.segments.max_size) != ""
+##If our min/max validation failed I trust MIRA to give an error message...
+templatesize = $rg.segments.min_size $rg.segments.max_size
+#end if
+#end if
+#if str($rg.segments.type) == "none"
+segmentplacement = ?
+#end if
 ##MIRA will accept multiple filenames on one data line, or multiple data lines
 #for $f in $rg.filenames
-#if str($rg.segment_placement) != ""
-##Record the segment placement (if any)
-segmentplacement = ${rg.segment_placement}
-#end if
 ##Must now map Galaxy datatypes to MIRA file types...
 #if $f.ext.startswith("fastq")
 ##MIRA doesn't like fastqsanger etc, just plain old fastq:
@@ -120,18 +149,35 @@
 
 It is particularly suited to small genomes such as bacteria.
 
-**Notes**
+
+**Notes on paired reads**
 
 .. class:: warningmark
 
-Note that the raw data for Roche 454 and Ion Torrent paired-end libraries
-sequences a circularised fragment such that the raw data starts with the
-end of the fragment, a linker, then the start of the fragment. This means
-both the start and end are sequenced from the same strand, and thus should
-be given to MIRA as orientation "2---&gt; 1---&gt;". However, in order to
-use this data with traditional tools expecting Sanger capillary style
-libraries which expect "---&gt; &lt;---" your FASTQ files may have been
-pre-processed to mimic this by reverse complementing one of the pair.
+MIRA uses read naming conventions to identify paired read partners
+(and does not care about their order in the input files). In most cases,
+the Solexa/Illumina setting is fine. For Sanger capillary sequencing,
+you may need to rename your reads to match one of the standard conventions
+supported by MIRA. For Roche 454 or Ion Torrent the appropriate settings
+depend on how the FASTQ file was produced:
+
+* If using Roche's ``sffinfo`` or older versions of ``sff_extract``
+  to convert SFF files to FASTQ, your reads will probably have the
+  ``---&gt; &lt;---`` orientation and use the ``.f`` and ``.r``
+  suffixes (FR naming).
+
+* If using a recent version of ``sff_extract``, then the ``/1`` and ``/2``
+  suffixes are used (Solexa/Illumina style naming) and the original
+  ``2---&gt; 1---&gt;`` orientation is preserved.
+
+The reason for this is the raw data for Roche 454 and Ion Torrent paired-end
+libraries sequences a circularised fragment such that the raw data begins
+with the end of the fragment, a linker, then the start of the fragment.
+This means both the start and end are sequenced from the same strand, and
+have the orientation ``2---&gt; 1---&gt;``. However, in order to use the data
+with traditional tools expecting Sanger capillary style ``---&gt; &lt;---``
+orientation it was common to reverse complement one of the pair to mimic this.
+
 
 **Citation**