diff hmmfetch.xml @ 0:1d78de693262 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hmmfetch.xml	Sat Jun 25 15:05:58 2016 -0400
@@ -0,0 +1,40 @@
+<?xml version="1.0"?>
+<tool id="hmmer_hmmfetch" name="hmmfetch" version="@WRAPPER_VERSION@.0">
+  <description>retrieve profile HMM(s) from a file</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+hmmfetch -f $hmmfile $keyfile > $output;
+      ]]></command>
+  <inputs>
+    <!-- TODO: implement auto-indexing -->
+    <expand macro="input_hmm" />
+    <param name="keyfile" type="data" format="tabular,txt" label="List of HMM names to extract"/>
+  </inputs>
+  <outputs>
+    <data format="hmm3" name="output" label="Selected HMM Models from $hmmfile.name">
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="hmmfile" value="fn3.hmm"/>
+      <param name="keyfile" value="fn3.keys"/>
+      <output name="output" file="fn3.hmm" lines_diff="4"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+@HELP_PRE@
+
+Quickly retrieves one or more profile HMMs from an <hmmfile> (a large Pfam
+database, for example). The profile names should be listed in a text file,
+separated by newlines
+
+By default, fetched HMMs are printed to standard output in HMMER3 format.
+
+@ATTRIBUTION@
+]]></help>
+  <expand macro="citation"/>
+</tool>