<?xml version="1.0"?>
<tool id="hmmer_hmmemit" name="hmmemit" version="@TOOL_VERSION@">
  <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 $oformat.N_smp
    -p
    #if str($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" argument="-N" type="integer" min="1" value="1"
                label="Number of sequences to generate"/>
        </when>
        <when value="aln">
            <param name="N_aln" argument="-N" type="integer" min="1" value="1"
                label="Number of sequences to generate"/>
        </when>
        <when value="mrcs" />
        <when value="mrcsf">
            <param argument="--minl" type="float" value="0.7"
                label="show consensus as 'any' (X/N) unless >= this fraction"/>
            <param argument="--minu" type="float" value="0.2"
                label="show consensus as upper case if >= this fraction"/>
        </when>
        <when value="sample">
            <param name="N_smp" argument="-N" type="integer" min="1" value="1"
                label="Number of sequences to generate"/>
            <param argument="-L" type="integer" optional="true"
                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 name="output" format="fasta" 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" compare="sim_size"/>
    </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" compare="sim_size"/>
    </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>