diff emboss_supermatcher.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_supermatcher.xml	Wed Feb 08 12:42:22 2017 -0500
@@ -0,0 +1,55 @@
+<tool id="EMBOSS: supermatcher95" name="supermatcher" version="5.0.0.1">
+  <!-- puts file information in output report -->
+  <description>Match large sequences against one or more other sequences</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command>supermatcher -asequence '$input1' -bsequence '$input2' -gapopen $gapopen -gapextend $gapextend -width $width -wordlen $wordlen -outfile '$ofile1' -errorfile '$ofile2' -aformat3
+  $out_format1 -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="Large sequences" />
+    <param name="input2" type="data" format="data" label="Sequences to match" />
+    <param name="gapopen" type="float" value="10.0" label="Gap opening penalty" />
+    <param name="gapextend" type="float" value="0.5" label="Gap extension penalty" />
+    <param name="width" type="integer" value="16" label="Alignment width" />
+    <param name="wordlen" type="integer" value="6" label="Word length for initial matching" />
+    <param name="out_format1" type="select" label="Output alignment file format">
+      <option value="simple">Simple (m)</option>
+      <option value="fasta">FASTA (m)</option>
+      <option value="msf">MSF (m)</option>
+      <option value="srs">SRS (m)</option>
+      <option value="pair">Pair (p)</option>
+      <option value="markx0">Markx0 (p)</option>
+      <option value="markx1">Markx1 (p)</option>
+      <option value="markx2">Markx2 (p)</option>
+      <option value="markx3">Markx3 (p)</option>
+      <option value="markx10">Markx10 (p)</option>
+      <option value="srspair">SRS pair (p)</option>
+      <option value="score">Score (p)</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="ofile1" format="simple" />
+    <data name="ofile2" format="supermatcher" />
+  </outputs>
+<!--    <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="input2" value="1.fasta"/>
+      <param name="gapopen" value="10.0"/>
+      <param name="gapextend" value="0.5"/>
+      <param name="width" value="16"/>
+      <param name="wordlen" value="6"/>
+      <param name="out_format1" value="fasta"/>
+      <output name="ofile1" file="emboss_supermatcher_out.fasta"/>
+    </test>
+  </tests> -->
+  <help>
+    You can view the original documentation here_.
+
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/supermatcher.html
+  </help>
+  <expand macro="citations" />
+</tool>