--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hmmemit.xml	Tue May 12 15:04:26 2015 -0400
@@ -0,0 +1,175 @@
+<?xml version="1.0"?>
+<tool id="hmmer_hmmemit" name="hmmemit" version="@WRAPPER_VERSION@.0">
+  <description>sample sequence(s) from a profile HMM</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+hmmemit
+
+#if $oformat.oformat_select == "fasta":
+    -N $oformat.N_fa
+#elif $oformat.oformat_select == "aln":
+    -N $oformat.N_aln
+    -a
+#elif $oformat.oformat_select == "mrcs":
+    -c
+#elif $oformat.oformat_select == "mrcsf":
+    --minl $oformat.minl
+    --minu $oformat.minu
+    -C
+#else:
+    -N $oformat.N_smp
+    -p
+    #if $oformat.L:
+        -L $oformat.L
+    #end if
+    $oformat.emission_profiles
+#end if
+
+
+@SEED@
+
+$hmmfile
+> $output
+      ]]></command>
+  <inputs>
+    <expand macro="input_hmm" />
+
+    <conditional name="oformat">
+        <param name="oformat_select" type="select" label="Output Format">
+            <option value="fasta" selected="true">Fasta</option>
+            <option value="aln">Alignment</option>
+            <option value="mrcs">Majority-Rule Concensus Sequence</option>
+            <option value="mrcsf">Fancier Concensus Sequence</option>
+            <option value="sample">Sample sequences from profile, not core model</option>
+        </param>
+        <when value="fasta">
+            <param name="N_fa" type="integer" value="1" min="1" help="(-N)"
+                label="Number of sequences to generate"/>
+        </when>
+        <when value="aln">
+            <param name="N_aln" type="integer" value="1" min="1" help="(-N)"
+                label="Number of sequences to generate"/>
+        </when>
+        <when value="mrcs">
+        </when>
+        <when value="mrcsf">
+            <param name="minl" type="float" value="0.7" help="(--minl)"
+                label="show consensus as 'any' (X/N) unless >= this fraction"/>
+            <param name="minu" type="float" value="0.2" help="(--minu)"
+                label="show consensus as upper case if >= this fraction"/>
+        </when>
+        <when value="sample">
+            <param name="N_smp" type="integer" value="1" min="1" help="(-N)"
+                label="Number of sequences to generate"/>
+            <param name="L" type="integer" optional="True" help="(-L)"
+                label="Expected length of profile"/>
+
+            <param name="emission_profiles" type="select" label="Emission profile options">
+                <option value="--local" selected="true">configure profile in multihit local mode</option>
+                <option value="--unilocal">configure profile in unilocal mode</option>
+                <option value="--glocal">configure profile in multihit glocal mode</option>
+                <option value="--uniglocal">configure profile in unihit glocal mode</option>
+            </param>
+        </when>
+    </conditional>
+
+
+    <expand macro="seed"/>
+  </inputs>
+  <outputs>
+    <data format="fasta" name="output" label="Sequences generated from $hmmfile.name">
+      <change_format>
+        <when input="oformat_select" value="aln" format="stockholm"/>
+        <!-- the rest are fasta -->
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="hmmfile" value="globins4.hmm"/>
+      <param name="oformat_select" value="aln"/>
+      <param name="N_aln" value="10"/>
+      <expand macro="seed_test" />
+      <output name="output" file="globins4-emit.sto" lines_diff="4"/>
+    </test>
+    <test>
+      <param name="hmmfile" value="globins4.hmm"/>
+      <param name="oformat_select" value="fasta"/>
+      <param name="N_aln" value="10"/>
+      <expand macro="seed_test" />
+      <output name="output" file="globins4-emit-1.sto" lines_diff="4"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+@HELP_PRE@
+
+The hmmemit program samples (emits) sequences from the profile HMM(s) in
+hmmfile, and writes them to output. Sampling sequences may be useful for a
+variety of purposes, including creating synthetic true positives for benchmarks
+or tests.
+
+The default is to sample one unaligned sequence from the core probability
+model, which means that each sequence consists of one full-length domain.
+Alternatively, with the -c option, you can emit a simple majority-rule
+consensus sequence; or with the -a option, you can emit an alignment (in which
+case, you probably also want to set -N to something other than its default of 1
+sequence per model).
+
+As another option, with the -p option you can sample a sequence from a fully
+configured HMMER search profile. This means sampling a ‘homologous sequence’ by
+HMMER’s definition, including nonhomologous flanking sequences, local
+alignments, and multiple domains per sequence, depending on the length model
+and alignment mode chosen for the profile.
+
+The hmmfile may contain a library of HMMs, in which case each HMM will be used
+in turn.
+
+@HELP_PRE_OTH@
+
+Output Formats
+--------------
+
+Several output formats are available, each with different options.
+
+**Fasta**
+
+Fasta option is the easiest to understand, given an input model, it will produce N sequences in fasta format from that model.
+
+**Alignment**
+
+Produces a stockholm alignment, of what the Fasta output would have produced.
+
+**Majority-Rule Concensus Sequence**
+
+Emit a plurality-rule consensus sequence, instead of sampling a sequence from
+the profile HMM’s probability distribution. The consensus sequence is formed by
+selecting the maximum probability residue at each match state.
+
+**Fancier Concensus Sequence**
+
+Emit a fancier plurality-rule consensus sequence than the -c option. If the
+maximum probability residue has p < minl show it as a lower case ’any’ residue
+(n or x); if p >= minl and < minu show it as a lower case residue; and if p >=
+minu show it as an upper case residue. The default settings of minu and minl
+are both 0.0, which means -C gives the same output as -c unless you also set
+minu and minl to what you want.
+
+**Sample**
+
+Sample unaligned sequences from the implicit search profile, not from the core
+model. The core model consists only of the homologous states (between the begin
+and end states of a HMMER Plan7 model). The profile includes the nonhomologous
+N, C, and J states, local/glocal and uni/multihit algorithm configuration, and
+the target length model. Therefore sequences sampled from a profile may in-
+clude nonhomologous as well as homologous sequences, and may contain more than
+one homologous sequence segment. By default, the profile is in multihit local
+mode, and the target sequence length is configured for L=400.
+
+@ATTRIBUTION@
+]]></help>
+  <expand macro="citation"/>
+</tool>