diff sspace.xml @ 0:b1be94418db9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sspace.xml	Tue Sep 17 09:41:18 2013 -0400
@@ -0,0 +1,113 @@
+<tool id="sspace" name="SSPACE" version="1.0.5">
+  <description>scaffolder</description>
+  <requirements>
+    <requirement type="package" version="2.0">sspace</requirement>
+  </requirements>
+
+  <command interpreter="python">
+    sspace.py
+    \${SSPACE_SITE_OPTIONS:--T 1}
+    -c $contigs --r1 $reads1 --r2 $reads2 -i $insert -e $error -o $orientation
+    #if $exten
+      -x
+    #end if
+    #if str($minoverlap)
+      --minoverlap $minoverlap
+    #end if
+    #if str($numofreads)
+      --numofreads $numofreads
+    #end if
+    #if str($max_trim)
+      -t $max_trim
+    #end if
+    #if $unpaired
+      -u $unpaired
+    #end if
+    #if str($min_base_ratio)
+      -r $min_base_ratio
+    #end if
+    #if str($minlink)
+      --minlink $minlink
+    #end if
+    #if str($maxratio)
+      --maxratio $maxratio
+    #end if
+    #if str($contigoverlap)
+      --contigoverlap $contigoverlap
+    #end if
+    #if str($mincontig)
+      --mincontig $mincontig
+    #end if
+    --lib $libraryname --fe $finalevidence --fs $finalscaffolds --lg $logfile --summ $summaryfile
+  </command>
+
+  <inputs>
+    <param name="contigs" type="data" format="fasta" label="Contigs FASTA file (-s)" />
+    <param name="reads1" type="data" format="fasta,fastq" label="Paired-end reads 1" help="FASTA or FASTQ format" />
+    <param name="reads2" type="data" format="fasta,fastq" label="Paired-end reads 2" help="FASTA or FASTQ format" />
+    <param name="insert" type="integer" value="" label="Insert size">
+      <validator type="in_range" min="1" />
+    </param>
+    <param name="error" type="float" min="0" max="1" value="" label="Variability (e.g. 0.25 for 25%)" />
+    <param name="orientation" type="select" label="Orientation">
+      <option value="FF">FF</option>
+      <option value="FR" selected="true">FR</option>
+      <option value="RF">RF</option>
+      <option value="RR">RR</option>
+    </param>
+    <param name="exten" type="boolean" checked="true" label="Extension (-x)" help="Uncheck for scaffolding only" />
+    <param name="minoverlap" type="integer" optional="true" min="10" max="50" value="35" label="Extension: minimum number of overlapping bases with the seed/contig during overhang consensus build up (-m)" help="E.g. 32-35 for 36bp reads" />
+    <param name="numofreads" type="integer" optional="true" value="8" label="Extension: minimum number of reads needed to call an extension (-o)" help="Higher numbers increase reliability of the extension">
+      <validator type="in_range" min="1" />
+    </param>
+    <param name="max_trim" type="integer" optional="true" value="0" label="Extension: maximum number of bases to trim on the contig end when all possibilities have been exhausted for an extension (-t)">
+      <validator type="in_range" min="0" />
+    </param>
+    <param name="unpaired" type="data" format="fasta,fastq" optional="true" label="Extension: unpaired reads (-u, optional)" help="FASTA or FASTQ format" />
+    <param name="min_base_ratio" type="float" optional="true" min="0" max="1" value="0.9" label="Extension: minimum base ratio used to accept a overhang consensus base (-r)" />
+    <param name="minlink" type="integer" optional="true" value="5" label="Scaffolding: minimum number of links (read pairs) to compute scaffold (-k)">
+      <validator type="in_range" min="0" />
+    </param>
+    <param name="maxratio" type="float" optional="true" min="0" max="1" value="0.7" label="Scaffolding: maximum link ratio between two best contig pairs (-a)" help="Higher values lead to less accurate scaffolding" />
+    <param name="contigoverlap" type="integer" optional="true" value="30" label="Scaffolding: minimum overlap required between contigs to merge adjacent contigs in a scaffold (-n)">
+      <validator type="in_range" min="0" />
+    </param>
+    <param name="mincontig" type="integer" optional="true" value="200" label="Scaffolding: minimum contig size used for scaffold (-z)" help="Filters out contigs below this size">
+      <validator type="in_range" min="0" />
+    </param>
+  </inputs>
+
+  <outputs>
+    <data name="libraryname" hidden="True" format="tabular" label="${tool.name} on ${on_string}: libraryfile" />
+    <data name="finalevidence" format="txt" label="${tool.name} on ${on_string}: final evidence" />
+    <data name="finalscaffolds" format="fasta" label="${tool.name} on ${on_string}: final scaffolds" />
+    <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
+    <data name="summaryfile" format="txt" label="${tool.name} on ${on_string}: summary" />
+  </outputs>
+  <tests>
+
+  </tests>
+  <help>
+**What it does**
+
+SSPACE is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired-end libraries, or even a combination.
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
+
+.. _CRS4 Srl.: http://www.crs4.it/
+.. _MIT license: http://opensource.org/licenses/MIT
+
+If you use this tool in Galaxy, please cite |Cuccuru2013|_.
+
+.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
+.. _Cuccuru2013: http://orione.crs4.it/
+
+This tool uses `SSPACE basic`_, which is licensed separately. Please cite |Boetzer2011|_.
+
+.. _SSPACE basic: http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/
+.. |Boetzer2011| replace:: Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D., Pirovano, W. (2011) Scaffolding pre-assembled contigs using SSPACE. *Bioinformatics* 27(4), 578-579
+.. _Boetzer2011: http://bioinformatics.oxfordjournals.org/content/27/4/578
+  </help>
+</tool>