diff hmmconvert.xml @ 0:62479bdcc059 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hmmconvert.xml	Tue May 12 15:04:26 2015 -0400
@@ -0,0 +1,49 @@
+<?xml version="1.0"?>
+<tool id="hmmer_hmmconvert" name="hmmconvert" version="@WRAPPER_VERSION@.0">
+  <description>convert profile file to a HMMER format</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+hmmconvert
+$format
+$hmmfile > $output
+      ]]></command>
+  <inputs>
+    <expand macro="input_hmm" />
+    <param type="select" label="Output Format" name="format">
+      <option value="-a" selected="true">output models in HMMER3 ASCII format</option>
+      <!--<option value="-b">output models in HMMER3 binary format</option>-->
+      <option value="-2">backward compatible HMMER2 ASCII format</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="hmmer3" name="output" label="$msafile.name">
+      <change_format>
+        <when input="format" value="-a" format="hmmer3"/>
+        <when input="format" value="-2" format="hmmer2"/>
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="msafile" value="globins4.hmm"/>
+      <param name="format" value="-2"/>
+      <output name="output" file="globins4.hmm2"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+@HELP_PRE@
+
+The hmmconvert utility converts an input profile file to different HMMER formats.
+
+By default, the input profile can be in any HMMER format, including
+old/obsolete formats from HMMER2, ASCII or binary; the output profile is a
+current HMMER3 ASCII format.
+
+@ATTRIBUTION@
+]]></help>
+  <expand macro="citation"/>
+</tool>