diff emboss_twofeat.xml @ 10:d49956b87f7e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emboss_twofeat.xml	Wed Feb 08 12:42:22 2017 -0500
@@ -0,0 +1,94 @@
+<tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0.1">
+  <description>Finds neighbouring pairs of features in sequences</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command>twofeat -sequence '$input1' -outfile '$out_file1' -atype '$atype' -btype '$btype' -minrange $minrange -maxrange $maxrange -asource '$asource' -asense $asense -aminscore $aminscore
+  -amaxscore $amaxscore -atag '$atag' -avalue '$avalue' -bsource '$bsource' -bsense $bsense -bminscore $bminscore -bmaxscore $bmaxscore -btag '$btag' -bvalue '$bvalue' -overlap $overlap
+  -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout '$typeout' -rformat2 $out_format1 -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="data" label="Sequences" />
+    <param name="atype" type="text" value="*" label="Feature type you wish to allow. Feature 1" />
+    <param name="btype" type="text" value="*" label="Feature type you wish to allow. Feature 2" />
+    <param name="minrange" type="integer" value="0" label="Minimun range" />
+    <param name="maxrange" type="integer" value="0" label="Maximum range" />
+    <param name="asource" type="text" value="*" label="Feature source 1" />
+    <param name="asense" type="select" label="Feature sense 1">
+      <option value="0">Any sense</option>
+      <option value="+">Forward sense</option>
+      <option value="-">Reverse sense</option>
+    </param>
+    <param name="aminscore" type="float" value="0.0" label="Feature 1 minimum score" />
+    <param name="amaxscore" type="float" value="0.0" label="Feature1 maximum score" />
+    <param name="atag" type="text" value="*" label="Feature 1 tags" />
+    <param name="avalue" type="text" value="*" label="Feature 1 tag values" />
+    <param name="bsource" type="text" value="*" label="Feature 2 source" />
+    <param name="bsense" type="select" label="Feature 2 sense">
+      <option value="0">Any sense</option>
+      <option value="+">Forward sense</option>
+      <option value="-">Reverse sense</option>
+    </param>
+    <param name="bminscore" type="float" value="0.0" label="Feature 2 minimum score" />
+    <param name="bmaxscore" type="float" value="0.0" label="Feature 2 maximum score" />
+    <param name="btag" type="text" value="*" label="Feature 2 tags" />
+    <param name="bvalue" type="text" value="*" label="Feature 2 tag values" />
+    <param name="overlap" type="select" label="Allowed overlaps">
+      <option value="A">Any</option>
+      <option value="O">Overlap required but not within</option>
+      <option value="NO">No overlaps are allowed</option>
+      <option value="NW:">Overlap required but not within</option>
+      <option value="AW">A must be all within B</option>
+      <option value="BW">B must be all within A</option>
+    </param>
+    <param name="rangetype" type="select" label="How to determine range">
+      <option value="N">From nearest ends</option>
+      <option value="L">From left ends</option>
+      <option value="R">From right ends</option>
+      <option value="F">From furthest ends</option>
+    </param>
+    <param name="sense" type="select" label="Required sense">
+      <option value="A">Any sense</option>
+      <option value="S">Same sense</option>
+      <option value="O">Opposite sense</option>
+    </param>
+    <param name="order" type="select" label="Required order of the two features">
+      <option value="A">Any</option>
+      <option value="AB">Feature A then feature B</option>
+      <option value="BA">Feature B then feature A</option>
+    </param>
+    <param name="twoout" type="select" label="Write out the two features themselves">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="typeout" type="text" value="misc_feature" label="New feature type" />
+    <param name="out_format1" type="select" label="Output report file format">
+      <option value="table">Table</option>
+      <option value="embl">EMBL</option>
+      <option value="genbank">GENBANK</option>
+      <option value="gff">GFF</option>
+      <option value="pir">PIR</option>
+      <option value="swiss">SwissProt</option>
+      <option value="dbmotif">DbMotif</option>
+      <option value="diffseq">Diffseq</option>
+      <option value="excel">Excel (tab delimited)</option>
+      <option value="feattable">FeatTable</option>
+      <option value="motif">Motif</option>
+      <option value="regions">Regions</option>
+      <option value="seqtable">SeqTable</option>
+      <option value="simple">SRS Simple</option>
+      <option value="srs">SRS</option>
+      <option value="tagseq">TagSeq</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="table" />
+  </outputs>
+  <help>
+    You can view the original documentation here_.
+
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/twofeat.html
+  </help>
+  <expand macro="citations" />
+</tool>