--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue May 12 15:04:26 2015 -0400
@@ -0,0 +1,1071 @@
+<?xml version="1.0"?>
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="3.1b1">hmmer3_1b1</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+  <token name="@WRAPPER_VERSION@">0.1</token>
+  <xml name="stdio">
+    <stdio>
+      <!-- Anything other than zero is an error -->
+      <exit_code range="1:"/>
+      <exit_code range=":-1"/>
+      <!-- In case the return code has not been set propery check stderr too -->
+      <regex match="Error:"/>
+      <regex match="Exception:"/>
+    </stdio>
+  </xml>
+  <token name="@THRESHOLDS@">
+-E $E
+--domE $domE
+
+#if $T:
+-T $T
+#end if
+
+#if $domT:
+--domT $domT
+#end if
+
+#if $incE:
+--incE $incE
+#end if
+
+#if $incT:
+--incT $incT
+#end if
+
+#if $incdomE:
+--incdomE $incdomE
+#end if
+
+#if $incdomT:
+--incdomT $incdomT
+#end if
+  </token>
+  <xml name="thresholds_xml">
+    <!-- Options controlling reporting thresholds -->
+    <param name="E" label="report sequences &lt;= this E-Value threshold in output" help="(-E)" value="10.0" type="float" min="0"/>
+    <param name="domE" label="report domains &lt;= this E-Value threshold in output" help="(--domE)" value="10.0" type="float" min="0"/>
+    <param name="T" label="report sequences &gt;= this score threshold in output" help="(-T)" type="float" optional="True"/>
+    <param name="domT" label="report domains &gt;= this score threshold in output" help="(--domT)" type="float" optional="True"/>
+    <!-- Options controlling inclusion (significance) thresholds -->
+    <param name="incE" label="consider sequences &lt;= this E-Value threshold as significant" help="(--incE)" type="float" optional="True"/>
+    <param name="incdomE" label="consider domains &lt;= this E-Value threshold as significant" help="(--incdomE)" type="float" optional="True"/>
+    <param name="incT" label="consider sequences &gt;= this score threshold as significant" help="(--incT)" type="float" optional="True"/>
+    <param name="incdomT" label="consider domains &gt;= this score threshold as significant" help="(--incdomT)" type="float" optional="True"/>
+  </xml>
+  <token name="@THRESHOLDS_NODOM@">
+-E $E
+
+#if $T:
+-T $T
+#end if
+
+#if $incE:
+--incE $incE
+#end if
+
+#if $incT:
+--incT $incT
+#end if
+  </token>
+  <xml name="thresholds_nodom">
+    <!-- Options controlling reporting thresholds -->
+    <param name="E" label="report sequences &lt;= this E-Value threshold in output" help="(-E)" value="10.0" type="float" min="0"/>
+    <param name="T" label="report sequences &gt;= this score threshold in output" help="(-T)" type="float" optional="True"/>
+    <!-- Options controlling inclusion (significance) thresholds -->
+    <param name="incE" label="consider sequences &lt;= this E-Value threshold as significant" help="(--incE)" type="float" optional="True"/>
+    <param name="incT" label="consider sequences &gt;= this score threshold as significant" help="(--incT)" type="float" optional="True"/>
+  </xml>
+  <token name="@ACCEL_HEUR@">
+$max
+--F1 $F1
+--F2 $F2
+--F3 $F3
+$nobias
+
+  </token>
+  <xml name="accel_heur_xml">
+    <!-- Options controlling acceleration heuristics -->
+    <param name="max" type="boolean" truevalue="--max" label="Turn all heuristic filters off (less speed, more power)" help="(--max)" falsevalue=""/>
+    <param name="F1" type="float" label="Stage 1 (MSV) threshold: promote hits w/ P &lt;= F1" help="(--F1)" value="0.02"/>
+    <param name="F2" type="float" label="Stage 2 (Vit) threshold: promote hits w/ P &lt;= F2" help="(--F2)" value="1e-3"/>
+    <param name="F3" type="float" label="Stage 3 (Fwd) threshold: promote hits w/ P &lt;= F3" help="(--F3)" value="1e-5"/>
+    <param name="nobias" type="boolean" truevalue="--nobias" label="Turn off composition bias filter" help="(--nobias)" falsevalue=""/>
+  </xml>
+  <token name="@EVAL_CALIB@">
+--EmL $EmL
+--EmN $EmN
+--EvL $EvL
+--EvN $EvN
+--EfL $EfL
+--EfN $EfN
+--Eft $Eft
+  </token>
+  <xml name="eval_calib_xml">
+    <!-- Control of E-value calibration -->
+    <param name="EmL" type="integer" value="200" min="1" help="(--EmL)" label="Length of sequences for MSV Gumbel mu fit"/>
+    <param name="EmN" type="integer" value="200" min="1" help="(--EmN)" label="Number of sequences for MSV Gumbel mu fit"/>
+    <param name="EvL" type="integer" value="200" min="1" help="(--EvL)" label="Length of sequences for Viterbi Gumbel mu fit"/>
+    <param name="EvN" type="integer" value="200" min="1" help="(--EvN)" label="Number of sequences for Viterbi Gumbel mu fit"/>
+    <param name="EfL" type="integer" value="100" min="1" help="(--EfL)" label="Length of sequences for Forward exp tail tau fit"/>
+    <param name="EfN" type="integer" value="200" min="1" help="(--EfN)" label="Number of sequences for Forward exp tail tau fit"/>
+    <param name="Eft" type="float" value="0.04" min="0" max="1" help="(--Eft)" label="tail mass for Forward exponential tail tau fit"/>
+  </xml>
+  <token name="@OFORMAT_WITH_OPTS_NOPFAM@">
+#if 'tblout' in str($oformat):
+    --tblout $tblout
+#end if
+
+#if 'domtblout' in str($oformat):
+    --domtblout $domtblout
+#end if
+
+$acc $noali $notextw
+  </token>
+  <xml name="oformat_with_opts_nopfam">
+    <!-- Options directing output -->
+    <param name="oformat" multiple="True" display="checkboxes" label="Output Formats" type="select">
+      <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
+      <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
+    </param>
+    <param name="acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" help="(--acc)"/>
+    <param name="noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" help="(--noali)"/>
+    <param name="notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" help="(--notextw)"/>
+  </xml>
+  <token name="@OFORMAT_WITH_OPTS@">
+#if 'tblout' in str($oformat):
+    --tblout $tblout
+#end if
+
+#if 'domtblout' in str($oformat):
+    --domtblout $domtblout
+#end if
+
+#if 'pfamtblout' in str($oformat):
+    --pfamtblout $pfamtblout
+#end if
+
+$acc $noali $notextw
+  </token>
+  <xml name="oformat_with_opts">
+    <!-- Options directing output -->
+    <param name="oformat" multiple="True" display="checkboxes" label="Output Formats" type="select">
+      <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
+      <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
+      <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option>
+    </param>
+    <param name="acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" help="(--acc)"/>
+    <param name="noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" help="(--noali)"/>
+    <param name="notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" help="(--notextw)"/>
+  </xml>
+  <xml name="oformat_test">
+      <param name="notextw" value="True" />
+  </xml>
+  <!-- TODO: tblout will match 'pfamtblout,dfamtblout' -->
+  <token name="@OFORMAT_WITH_OPTS_N@">
+#if 'tblout' in str($oformat):
+    --tblout $tblout
+#end if
+
+#if 'dfamtblout' in str($oformat):
+    --dfamtblout $dfamtblout
+#end if
+
+#if 'aliscoresout' in str($oformat):
+    --aliscoresout $aliscoresout
+#end if
+
+$acc $noali $notextw
+  </token>
+  <xml name="oformat_with_opts_n">
+    <!-- Options directing output -->
+    <param name="oformat" multiple="True" display="checkboxes" label="Output Formats" type="select">
+      <option value="tblout" selected="true">Table of hits (--tblout)</option>
+      <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option>
+      <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option>
+    </param>
+    <param name="acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" help="(--acc)"/>
+    <param name="noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" help="(--noali)"/>
+    <param name="notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" help="(--notextw)"/>
+  </xml>
+  <token name="@HSSI@">
+#if $hssi.hssi_select == "singlemx":
+    --popen $hssi.popen
+    --pextend $hssi.pextend
+#end if
+  </token>
+  <xml name="hssi">
+    <!-- Handling single sequence inputs -->
+    <conditional name="hssi">
+      <param name="hssi_select" type="select" label="Options for handling single sequence inputs">
+        <option value="false" selected="true">Disable</option>
+        <option value="singlemx">Use substitution score matrix for single-sequence inputs</option>
+      </param>
+      <when value="singlemx">
+        <param name="popen" type="float" value="0.02" label="Gap open probability" help="(--popen)" min="0.0" max="0.5"/>
+        <param name="pextend" type="float" value="0.4" label="Gap extend probability" help="(--pextend)" min="0.0" max="1.0"/>
+      </when>
+      <when value="false">
+      </when>
+      <!-- -mx <s>      : substitution score matrix (built-in matrices, with -singlemx)-->
+      <!-- -mxfile <f>  : read substitution score matrix from file <f> (with -singlemx)-->
+    </conditional>
+  </xml>
+  <token name="@CPU@">
+      --cpu \${GALAXY_SLOTS:-2}
+  </token>
+  <token name="@SEED@">
+      --seed $seed
+  </token>
+  <xml name="seed">
+    <param name="seed" label="RNG seed, 0 generates a random seed" value="42" type="integer" help="(--seed)" min="0"/>
+  </xml>
+  <xml name="seed_test">
+      <param name="seed" value="4" />
+  </xml>
+  <token name="@ADV_OPTS@">
+$nonull2
+
+#if $Z:
+-Z $Z
+#end if
+
+#if $domZ:
+--domZ $domZ
+#end if
+  </token>
+  <xml name="adv_opts">
+    <!-- Other options -->
+    <param name="nonull2" type="boolean" truevalue="--nonull2" label="Turn off biased composition score corrections" help="(--nonull2)" falsevalue=""/>
+    <param name="Z" type="integer" label="# of comparisons done for E-value calculation" help="(-Z)" optional="True"/>
+    <param name="domZ" type="integer" label="# of significant sequences, for domain E-value calculation" help="(--domZ)" optional="True"/>
+  </xml>
+  <token name="@FORMAT_SELECTOR@">
+      $input_format_select
+  </token>
+  <xml name="format_selector">
+    <param name="input_format_select" type="select" label="Format of sequence and model">
+      <option value="--amino">Protein</option>
+      <option value="--dna">DNA</option>
+      <option value="--rna">RNA</option>
+    </param>
+  </xml>
+  <xml name="format_selector_noprot">
+    <param name="input_format_select" type="select" label="Format of sequence and model">
+      <option value="--dna">DNA</option>
+      <option value="--rna">RNA</option>
+    </param>
+  </xml>
+  <token name="@ARSWS@">
+$arsws.arsws_select
+
+#if $arsws.arsws_select == "--wblosum":
+--wid $arsws.wid
+#end if
+  </token>
+  <xml name="arsws">
+    <!-- Alternative relative sequence weighting strategies -->
+    <conditional name="arsws">
+      <param name="arsws_select" type="select" label="Alternative relative sequence weighting strategies">
+        <option value="--wpb" selected="true">Henikoff position-based weights (--wpb)</option>
+        <option value="--wgsc">Gerstein/Sonnhammer/Chothia tree weights (--wgsc)</option>
+        <option value="--wblosum">Henikoff simple filter weights (--wblosum)</option>
+        <option value="--wnone">don't do any relative weighting; set all to 1 (--wnnoe)</option>
+        <option value="--wgiven">use weights as given in MSA file (--wgiven)</option>
+      </param>
+      <when value="--wpb">
+      </when>
+      <when value="--wgsc">
+      </when>
+      <when value="--wblosum">
+        <param name="wid" label="Set identity cutoff" value="0.62" type="float" help="(--wid)"/>
+      </when>
+      <when value="--wnone">
+      </when>
+      <when value="--wgiven">
+      </when>
+    </conditional>
+  </xml>
+  <token name="@AEEWS@">
+#if $aeews.aeews_select != "":
+--$aeews.aeews_select
+    #if $aeews.aeews_select == "eent":
+        --eset $aeews.eset
+        --ere $aeews.ere
+        --esigma $aeews.esigma
+    #elif $aeews.aeews_select == "eclust":
+        --eset $aeews.eset
+        --eid $aeews.eid
+    #end if
+#end if
+  </token>
+  <xml name="aeews">
+    <!-- Alternative effective sequence weighting strategies -->
+    <conditional name="aeews">
+      <param name="aeews_select" type="select" label="Alternative effective sequence weighting strategies">
+        <option value="">Disabled</option>
+        <option value="eent">Adjust eff seq # to achieve relative entropy target (--eent)</option>
+        <option value="eclust">Eff seq # is the # of single linkage clusters (--eclust)</option>
+        <option value="enone">No effective seq # weighting: just use nseq (--enone)</option>
+      </param>
+      <when value="">
+      </when>
+      <when value="eent">
+        <param name="eset" type="float" value="0" label="set eff seq # for all models" help="(--eset)"/>
+        <param name="ere" type="float" value="0" label="set minimum rel entropy/position" help="(--ere)"/>
+        <param name="esigma" type="float" value="45" label="set sigma param" help="(--esigma)"/>
+      </when>
+      <when value="eclust">
+        <param name="eset" type="float" value="0" label="set eff seq # for all models" help="(--eset)"/>
+        <param name="eid" type="float" value="0.62" label="set fractional identity cutoff" min="0" max="1" help="(--eid)"/>
+      </when>
+      <when value="enone">
+      </when>
+    </conditional>
+  </xml>
+  <token name="@CUT@">
+$cut_ga
+$cut_nc
+$cut_tc
+  </token>
+  <xml name="cut">
+    <param name="cut_ga" type="boolean" truevalue="--cut_ga" label="use profile's GA gathering cutoffs to set all thresholding" help="(--cut_ga)" falsevalue=""/>
+    <param name="cut_nc" type="boolean" truevalue="--cut_nc" label="use profile's NC gathering cutoffs to set all thresholding" help="(--cut_nc)" falsevalue=""/>
+    <param name="cut_tc" type="boolean" truevalue="--cut_tc" label="use profile's TC gathering cutoffs to set all thresholding" help="(--cut_tc)" falsevalue=""/>
+  </xml>
+  <token name="@MCSS@">
+--$mcs.model_construction_strategy_select
+
+#if $mcs.model_construction_strategy_select == "fast":
+--symfrac $mcs.symfrac
+#end if
+
+  </token>
+  <xml name="mcss">
+    <!-- Alternative model construction strategies -->
+    <conditional name="mcs">
+      <param name="model_construction_strategy_select" type="select" label="Model Construction Strategy">
+        <option value="fast" selected="true">Assign columns with &gt;= symfrac residues as consensus (--fast)</option>
+        <option value="hand">Manual construction (requires reference annotation) (--hand)</option>
+      </param>
+      <when value="fast">
+        <param name="symfrac" value="0.5" type="float" label="Sets sym fraction controlling --fast construction"/>
+      </when>
+      <when value="hand"></when>
+    </conditional>
+    <param name="fragthresh" label="Fraction of alignment length, under which sequences are excluded" help="HMMER infers fragments if the sequence length L is less than or equal to a fraction x times the alignment length in columns (--fragthresh)" value="0.5" optional="True" type="float" />
+
+  </xml>
+  <token name="@PRIOR@">
+$aps_select
+  </token>
+  <xml name="prior">
+    <param name="aps_select" type="select" label="Alternative Prior Strategies">
+      <option value="" selected="true">Unspecified</option>
+      <option value="--pnone">Don't use any prior; parameters are frequencies (--pnone)</option>
+      <option value="--plaplace">Use a Laplace +1 prior (--plaplace)</option>
+    </param>
+  </xml>
+  <xml name="citation">
+    <citations>
+      <citation type="doi">10.1093/nar/gkr367</citation>
+    </citations>
+  </xml>
+  <token name="@LENGTHS@">
+#if $w_beta:
+--w_beta $w_beta
+#end if
+
+#if $w_length:
+--w_length $w_length
+#end if
+
+  </token>
+  <xml name="lengths">
+    <param name="w_beta" label="Tail mass at which window length is determined"
+        help="(--w_beta)" optional="True" type="float"/>
+    <param name="w_length" label="Window Length"
+        help="(--w_length)" optional="True" type="integer" />
+  </xml>
+  <xml name="input_hmm">
+    <param name="hmmfile" type="data" label="HMM model" format="hmmer2,hmmer3"/>
+  </xml>
+  <xml name="input_msa">
+    <param name="msafile" type="data" label="MSA File" format="stockholm"/>
+  </xml>
+
+
+  <token name="@ACCEL_HEUR_HELP@"><![CDATA[
+Acceleration Heuristicts (--F1, --F2, --F3)
+-------------------------------------------
+
+**MSV filter**
+
+The sequence is aligned to the profile using a specialized model that
+allows multiple high-scoring local ungapped segments to match. The
+optimal alignment score (Viterbi score) is calculated under this multi-
+segment model, hence the term MSV, for “multi-segment Viterbi”. This is
+HMMER’s main speed heuristic. The MSV score is comparable to BLAST’s sum
+score (optimal sum of ungapped alignment segments). Roughly speaking,
+MSV is comparable to skipping the heuristic word hit and hit extension
+steps of the BLAST acceleration algorithm.
+
+The MSV filter is very, very fast. In addition to avoiding indel
+calculations in the dynamic programming table, it uses reduced precision
+scores scaled to 8-bit integers, enabling acceleration via 16-way
+parallel SIMD vector instructions.
+
+The MSV score is a true log-odds likelihood ratio, so it obeys
+conjectures about the expected score distribution (Eddy, 2008) that
+allow immediate and accurate calculation of the statistical significance
+(P- value) of the MSV bit score.
+
+By default, comparisons with a P-value of ≤ 0.02 pass this filter,
+meaning that about 2% of nonhomol- ogous sequences are expected to pass.
+You can use the --F1 option to change this threshold. For example, --F1
+<0.05> would pass 5% of the comparisons, making a search more sensitive
+but slower. Setting the threshold to ≥ 1.0 (--F1 99 for example) assures
+that all comparisons will pass. Shutting off the MSV filter may be
+worthwhile if you want to make sure you don’t miss comparisons that have
+a lot of scattered insertions and deletions. Alternatively, the --max
+option causes the MSV filter step (and all other filter steps) to be
+bypassed.
+
+The MSV bit score is calculated as a log-odds score using the null model
+for comparison. No correction for a biased composition or repetitive
+sequence is done at this stage. For comparisons involving biased
+sequences and/or profiles, more than 2% of comparisons will pass the MSV
+filter. At the end of search output, there is a line like:
+
+    Passed MSV filter: 107917 (0.020272); expected 106468.8 (0.02)
+
+which tells you how many and what fraction of comparisons passed the MSV
+filter, versus how many (and what fraction) were expected.
+
+**Viterbi filter**
+
+The sequence is now aligned to the profile using a fast Viterbi algorithm for
+optimal gapped alignment.
+
+This Viterbi implementation is specialized for speed. It is implemented in
+8-way parallel SIMD vector instructions, using reduced precision scores that
+have been scaled to 16-bit integers. Only one row of the dynamic programming
+matrix is stored, so the routine only recovers the score, not the optimal
+alignment itself. The reduced representation has limited range; local alignment
+scores will not underflow, but high scoring comparisons can overflow and return
+infinity, in which case they automatically pass the filter.
+
+The final Viterbi filter bit score is then computed using the appropriate null
+model log likelihood (by default the biased composition filter model score, or
+if the biased filter is off, just the null model score). If the P-value of this
+score passes the Viterbi filter threshold, the sequence passes on to the next
+step of the pipeline.
+
+The --F2 <x> option controls the P-value threshold for passing the Viterbi
+filter score. The default is 0.001. The --max option bypasses all filters in
+the pipeline.  At the end of a search output, you will see a line like:
+
+    Passed Vit filter: 2207  (0.00443803); expected 497.3 (0.001)
+
+which tells you how many and what fraction of comparisons passed the Viterbi
+filter, versus how many were expected.
+
+**Forward filter/parser**
+
+The sequence is now aligned to the profile using the full Forward algorithm,
+which calculates the likelihood of the target sequence given the profile,
+summed over the ensemble of all possible alignments.
+
+This is a specialized time- and memory-efficient Forward implementation called
+the “Forward parser”. It is implemented in 4-way parallel SIMD vector
+instructions, in full precision (32-bit floating point). It stores just enough
+information that, in combination with the results of the Backward parser
+(below), posterior probabilities of start and stop points of alignments
+(domains) can be calculated in the domain definition step (below), although the
+detailed alignments themselves cannot be.
+
+The Forward filter bit score is calculated by correcting this score using the
+appropriate null model log likelihood (by default the biased composition filter
+model score, or if the biased filter is off, just the null model score). If the
+P-value of this bit score passes the Forward filter threshold, the sequence
+passes on to the next step of the pipeline.
+
+The bias filter score has no further effect in the pipeline. It is only used in
+filter stages. It has no effect on final reported bit scores or P-values.
+Biased composition compensation for final bit scores is done by a more complex
+domain-specific algorithm, described below.
+
+The --F3 <x> option controls the P-value threshold for passing the Forward
+filter score. The default is 1e-5. The --max option bypasses all filters in the
+pipeline.  At the end of a search output, you will see a line like:
+
+    Passed Fwd filter: 1076 (0.00216371); expected 5.0 (1e-05)
+
+which tells you how many and what fraction of comparisons passed the Forward
+filter, versus how many were expected.
+
+**Bias Filter Options**
+
+The --max option bypasses all filters in the pipeline, including the bias
+filter.
+
+The --nobias option turns off (bypasses) the biased composition filter. The
+simple null model is used as a null hypothesis for MSV and in subsequent filter
+steps. The biased composition filter step compromises a small amount of
+sensitivity. Though it is good to have it on by default, you may want to shut
+it off if you know you will have no problem with biased composition hits.
+
+
+**Advanced Documentation**
+
+A more detailed look at the internals of the various filter pipelines was
+posted on the `developer's blog <http://selab.janelia.org/people/eddys/blog/?p=508>`__.
+The information posted there may be useful to those who are struggling with
+poor-scoring sequences.
+
+]]></token>
+  <token name="@ADV_OPTS_HELP@"><![CDATA[
+Advanced Options
+----------------
+
+**nonull2**
+
+can be too aggressive sometimes, causing you to miss homologs. You can turn the
+biased-composition score correction off with the --nonull2 option (and if
+you’re doing that, you may also want to set --nobias, to turn off another
+biased composition step called the bias filter, which affects which sequences
+get scored at all).
+
+**domZ**
+
+Assert that the total number of targets in your searches is <x>, for the
+purposes of per-domain conditional E-value calculations, rather than the number
+of targets that passed the reporting thresholds.
+
+**Z**
+
+Assert that the total number of targets in your searches is <x>, for the
+purposes of per-sequence E-value calculations, rather than the actual number of
+targets seen.
+]]></token>
+  <token name="@AEEWS_HELP@"><![CDATA[
+Effective Sequence Number
+-------------------------
+
+After relative weights are determined, they are normalized to sum to a total
+effective sequence number, eff nseq. This number may be the actual number of
+sequences in the alignment, but it is almost always smaller than that. The
+default entropy weighting method (--eent) reduces the effective sequence num-
+ber to reduce the information content (relative entropy, or average expected
+score on true homologs) per consensus position. The target relative entropy is
+controlled by a two-parameter function, where the two parameters are settable
+with --ere and --esigma.
+
+**--eent**
+
+Adjust effective sequence number to achieve a specific relative entropy per
+position (see --ere). This is the default.
+
+**--eclust**
+
+Set effective sequence number to the number of single-linkage clusters at a
+specific identity threshold (see --eid). This option is not recommended; it’s
+for experiments evaluating how much better --eent is.
+
+**--enone**
+
+Turn off effective sequence number determination and just use the actual number
+of sequences. One reason you might want to do this is to try to maximize the
+relative entropy/position of your model, which may be useful for short models.
+
+**--eset**
+
+Explicitly set the effective sequence number for all models to <x>.
+
+**--ere**
+
+Set the minimum relative entropy/position target to <x>. Requires --eent. Default
+depends on the sequence alphabet. For protein sequences, it is 0.59 bits/position;
+for nucleotide sequences, it is 0.45 bits/position.
+
+**--esigma**
+
+Sets the minimum relative entropy contributed by an entire model alignment, over
+its whole length. This has the effect of making short models have higher relative
+entropy per position than --ere alone would give. The default is 45.0 bits.
+
+**--eid**
+
+Sets the fractional pairwise identity cutoff used by single linkage clustering
+with the --eclust option. The default is 0.62.
+]]></token>
+  <token name="@ARSWS_HELP@"><![CDATA[
+Options Controlling Relative Weights
+------------------------------------
+
+HMMER uses an ad hoc sequence weighting algorithm to downweight closely related
+sequences and up-weight distantly related ones. This has the effect of making
+models less biased by uneven phylogenetic representation. For example, two
+identical sequences would typically each receive half the weight that one
+sequence would. These options control which algorithm gets used.
+
+
+**--wpb**
+
+Use the Henikoff position-based sequence weighting scheme [Henikoff and
+Henikoff, J. Mol. Biol. 243:574, 1994]. This is the default.
+
+**--wgsc**
+
+Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Gerstein et al, J.
+Mol. Biol. 235:1067, 1994].
+
+**--wblosum**
+
+Use the same clustering scheme that was used to weight data in calculating
+BLOSUM subsitution matrices [Henikoff and Henikoff, Proc. Natl. Acad. Sci
+89:10915, 1992]. Sequences are single-linkage clustered at an identity
+threshold (default 0.62; see --wid) and within each cluster of c sequences,
+each sequence gets rela- tive weight 1/c.
+
+**--wnone**
+
+No relative weights. All sequences are assigned uniform weight.
+
+**--wid**
+
+Sets the identity threshold used by single-linkage clustering when using
+--wblosum.  Invalid with any other weighting scheme. Default is 0.62.
+]]></token>
+  <token name="@BIAS_COMP_HELP@"><![CDATA[
+Bias Composition
+----------------
+
+The next number, the bias, is a correction term for biased sequence composition
+that has been applied to the sequence bit score.1 For instance, for the top hit
+MYG PHYCA that scored 222.7 bits, the bias of 3.2 bits means that this sequence
+originally scored 225.9 bits, which was adjusted by the slight 3.2 bit biased-
+composition correction. The only time you really need to pay attention to the
+bias value is when it’s large, on the same order of magnitude as the sequence
+bit score. Sometimes (rarely) the bias correction isn’t aggressive enough, and
+allows a non-homolog to retain too much score.  Conversely, the bias correction
+can be too aggressive sometimes, causing you to miss homologs. You can turn the
+biased-composition score correction off with the --nonull2 option (and if
+you’re doing that, you may also want to set --nobias, to turn off another
+biased composition step called the bias filter, which affects which sequences
+get scored at all).
+
+]]></token>
+  <token name="@CUT_HELP@"><![CDATA[
+Options for Model-specific Score Thresholding
+---------------------------------------------
+
+Curated profile databases may define specific bit score thresholds for each
+profile, superseding any thresholding based on statistical significance alone.
+To use these options, the profile must contain the appropriate (GA, TC, and/or
+NC) optional score threshold annotation; this is picked up by hmmbuild from
+Stockholm format alignment files. Each thresholding option has two scores: the
+per-sequence threshold <x1> and the per-domain threshold <x2> These act as if
+-T<x1> --incT<x1> --domT<x2> --incdomT<x2> has been applied specifically using
+each model’s curated thresholds.
+
+**--cut_ga**
+
+Use the GA (gathering) bit scores in the model to set per-sequence (GA1) and
+per-domain (GA2) reporting and inclusion thresholds. GA thresholds are
+generally considered to be the reliable curated thresholds defining family
+membership; for example, in Pfam, these thresholds define what gets included in
+Pfam Full alignments based on searches with Pfam Seed models.
+
+**--cut_nc**
+
+Use the NC (noise cutoff) bit score thresholds in the model to set
+per-sequence (NC1) and per-domain (NC2) reporting and inclusion thresholds. NC
+thresholds are generally considered to be the score of the highest-scoring
+known false positive.
+
+**--cut_tc**
+
+Use the NC (trusted cutoff) bit score thresholds in the model to set
+per-sequence (TC1) and per-domain (TC2) reporting and inclusion thresholds. TC
+thresholds are generally considered to be the score of the lowest-scoring known
+true positive that is above all known false positives.
+]]></token>
+  <token name="@EVAL_CALIB_HELP@"><![CDATA[
+Options Controlling H3 Parameter Estimation Methods
+---------------------------------------------------
+
+H3 uses three short random sequence simulations to estimating the location
+parameters for the expected score distributions for MSV scores, Viterbi scores,
+and Forward scores. These options allow these simulations to be modified.
+
+**--EmL**
+
+Sets the sequence length in simulation that estimates the location parameter mu
+for MSV E-values. Default is 200.
+
+**--EmN**
+
+Sets the number of sequences in simulation that estimates the location parameter
+mu for MSV E-values. Default is 200.
+
+**--EvL**
+
+Sets the sequence length in simulation that estimates the location parameter mu
+for Viterbi E-values. Default is 200.
+
+**--EvN**
+
+Sets the number of sequences in simulation that estimates the location parameter
+mu for Viterbi E-values. Default is 200.
+
+
+**--EfL**
+
+Sets the sequence length in simulation that estimates the location parameter tau
+for Forward E-values. Default is 100.
+
+**--EfN**
+
+Sets the number of sequences in simulation that estimates the location parameter
+tau for Forward E-values. Default is 200.
+
+**--Eft**
+
+Sets the tail mass fraction to fit in the simulation that estimates the location param-
+eter tau for Forward evalues. Default is 0.04.
+]]></token>
+  <token name="@FORMAT_SELECTOR_HELP@"><![CDATA[
+Options for Specifying the Alphabet
+-----------------------------------
+
+The alphabet type (amino, DNA, or RNA) is autodetected by default, by looking
+at the composition of the msafile. Autodetection is normally quite reliable,
+but occasionally alphabet type may be ambiguous and autodetection can fail (for
+instance, on tiny toy alignments of just a few residues). To avoid this, or to
+increase robustness in automated analysis pipelines, you may specify the
+alphabet type of msafile with these options.
+]]></token>
+  <token name="@HSSI_HELP@"><![CDATA[
+Options Controlling Single Sequence Scoring (first Iteration)
+-------------------------------------------------------------
+
+By default, the first iteration uses a search model constructed from a single
+query sequence. This model is constructed using a standard 20x20 substitution
+matrix for residue probabilities, and two additional pa- rameters for
+position-independent gap open and gap extend probabilities. These options allow
+the default single-sequence scoring parameters to be changed.
+
+**Gap Open (--popen)**
+
+Set the gap open probability for a single sequence query model to <x>
+
+**Gap Extend (--pextend)**
+
+Set the gap extend probability for a single sequence query model to <x>.
+
+
+**--mx/--mxfile**
+
+These options are not currently supported
+]]></token>
+  <token name="@LENGTHS_HELP@"><![CDATA[
+Tail Mass Options
+-----------------
+
+**Window length tail mass (--w_beta)**
+
+The upper bound, W, on the length at which nhmmer expects to find an instance
+of the model is set such that the fraction of all sequences generated by the
+model with length >= W is less than <x>. The default is 1e-7.
+
+
+**Model instance length upper bound (--w length)**
+
+Override the model instance length upper bound, W, which is otherwise
+controlled by --w beta. It should be larger than the model length. The value of
+W is used deep in the acceleration pipeline, and modest changes are not
+expected to impact results (though larger values of W do lead to longer run
+time).
+
+]]></token>
+  <token name="@MCSS_HELP@"><![CDATA[
+**Options Controlling Profile Construction**
+
+These options control how consensus columns are defined in an alignment.
+
+**--fast**
+
+Define consensus columns as those that have a fraction >= symfrac of residues
+as opposed to gaps. (See below for the --symfrac option.) This is the default.
+
+**--hand**
+
+Define consensus columns in next profile using reference annotation to the multiple
+alignment. This allows you to define any consensus columns you like.
+
+
+**--symfrac**
+
+Define the residue fraction threshold necessary to define a consensus column
+when using the --fast option. The default is 0.5. The symbol fraction in each
+column is calculated after taking relative sequence weighting into account, and
+ignoring gap characters corresponding to ends of sequence fragments (as opposed
+to internal insertions/deletions). Setting this to 0.0 means that every
+alignment column will be assigned as consensus, which may be useful in some
+cases. Setting it to 1.0 means that only columns that include 0 gaps (internal
+insertions/deletions) will be assigned as consensus.
+
+**--fragthresh**
+
+We only want to count terminal gaps as deletions if the aligned sequence is
+known to be full-length, not if it is a fragment (for instance, because only
+part of it was sequenced). HMMER uses a simple rule to infer fragments: if the
+sequence length L is less than or equal to a fraction <x> times the alignment
+length in columns, then the sequence is handled as a fragment. The default is
+0.5. Setting --fragthresh0 will define no (nonempty) sequence as a fragment;
+you might want to do this if you know you’ve got a carefully curated alignment
+of full-length sequences. Setting --fragthresh1 will define all sequences as
+fragments; you might want to do this if you know your alignment is entirely
+composed of fragments, such as translated short reads in metagenomic shotgun
+data.
+
+]]></token>
+  <token name="@OFORMAT_WITH_OPTS_HELP@"><![CDATA[
+Options for Controlling Output
+------------------------------
+
+**Table of hits**
+
+Save a simple tabular (space-delimited) file summarizing the per-target output, with
+one data line per homologous target model found.
+
+**Table of per-domain hits**
+
+Save a simple tabular (space-delimited) file summarizing the per-domain output,
+with one data line per homologous domain detected in a query sequence for each
+homologous model.
+
+**Table of hits and domains in Pfam Format**
+
+Save an especially succinct tabular (space-delimited) file summarizing the
+per-target output, with one data line per homologous target model found.
+]]></token>
+  <token name="@OFORMAT_WITH_OPTS_NOPFAM_HELP@"><![CDATA[
+Options for Controlling Output
+------------------------------
+
+**Table of hits**
+
+Save a simple tabular (space-delimited) file summarizing the per-target output, with
+one data line per homologous target model found.
+
+**Table of per-domain hits**
+
+Save a simple tabular (space-delimited) file summarizing the per-domain output,
+with one data line per homologous domain detected in a query sequence for each
+homologous model.
+]]></token>
+  <token name="@OFORMAT_WITH_OPTS_N_HELP@"><![CDATA[
+Options for Controlling Output
+------------------------------
+
+**Table of hits**
+
+Save a simple tabular (space-delimited) file summarizing the per-target output, with
+one data line per homologous target model found.
+
+**Table of hits (dfam)**
+
+Save a tabular (space-delimited) file summarizing the per-hit output, similar
+to --tblout but more succinct.
+
+
+**List of per-position scores for each hit (--aliscoreout)**
+
+Save to file a list of per-position scores for each hit. This is useful, for
+example, in identifying regions of high score density for use in resolving
+overlapping hits from different models.
+
+]]></token>
+  <token name="@PRIOR_HELP@"><![CDATA[
+Options Controlling Priors
+--------------------------
+
+By default, weighted counts are converted to mean posterior probability
+parameter estimates using mixture Dirichlet priors. Default mixture Dirichlet
+prior parameters for protein models and for nucleic acid (RNA and DNA) models
+are built in. The following options allow you to override the default priors.
+
+**No priors (--pnone)**
+
+Don’t use any priors. Probability parameters will simply be the observed
+frequencies, after relative sequence weighting.
+
+**Laplace +1 prior**
+
+Use a Laplace +1 prior in place of the default mixture Dirichlet prior.
+]]></token>
+  <token name="@SEED_HELP@"><![CDATA[
+Random Seeding
+--------------
+
+Seed the random number generator with <n>, an integer >= 0. If <n> is nonzero,
+any stochastic simulations will be reproducible; the same command will give the
+same results. If <n> is 0, the random number generator is seeded arbitrarily,
+and stochastic simulations will vary from run to run of the same command.
+
+]]></token>
+  <token name="@THRESHOLDS_HELP@"><![CDATA[
+Options for Reporting Thresholds
+--------------------------------
+
+Reporting thresholds control which hits are reported in output files (the main
+output, --tblout, and --domtblout).
+
+**E-value (-E)**
+
+In the per-target output, report target profiles with an E-value of <= <x>. The
+default is 10.0, meaning that on average, about 10 false positives will be
+reported per query, so you can see the top of the noise and decide for yourself
+if it’s really noise.
+
+**Bit score (-T)**
+
+Instead of thresholding per-profile output on E-value, instead report target profiles
+with a bit score of >= <x>.
+
+**domain E-value (--domE)**
+
+In the per-domain output, for target profiles that have already satisfied the
+per-profile reporting threshold, report individual domains with a conditional
+E-value of <= <x>. The default is 10.0. A conditional E-value means the
+expected number of additional false positive domains in the smaller search
+space of those comparisons that already satisfied the per-profile reporting
+threshold (and thus must have at least one homologous domain already).
+
+**domain Bit scores (--domT)**
+
+Instead of thresholding per-domain output on E-value, instead report domains
+with a bit score of >= <x>.
+
+Options for Inclusion Thresholds
+--------------------------------
+
+Inclusion thresholds are stricter than reporting thresholds. Inclusion
+thresholds control which hits are considered to be reliable enough to be
+included in an output alignment or a subsequent search round. In hmmscan, which
+does not have any alignment output (like hmmsearch or phmmer) nor any iterative
+search steps (like jackhmmer), inclusion thresholds have little effect. They
+only affect what domains get marked as significant (!) or questionable (?) in
+domain output.
+
+**E-value of per target inclusion threshold**
+
+Use an E-value of <= <x> as the per-target inclusion threshold. The default is
+0.01, meaning that on average, about 1 false positive would be expected in
+every 100 searches with different query sequences.
+
+**Bit score of per target inclusion threshold**
+
+Instead of using E-values for setting the inclusion threshold, instead use a
+bit score of >= <x> as the per-target inclusion threshold. It would be unusual
+to use bit score thresholds with hmmscan, because you don’t expect a single
+score threshold to work for different profiles; different profiles have
+slightly different expected score distributions.
+
+**domain E-value per target inclusion treshold**
+
+Use a conditional E-value of <= <x> as the per-domain inclusion threshold, in
+targets that have already satisfied the overall per-target inclusion threshold.
+
+**domain Bit score per target inclusion treshold**
+
+Instead of using E-values, instead use a bit score of >= <x> as the per-domain
+inclusion threshold. As with --incT above, it would be unusual to use a single
+bit score threshold in hmmscan.
+
+]]></token>
+  <token name="@THRESHOLDS_NODOM_HELP@"><![CDATA[
+Options for Reporting Thresholds
+--------------------------------
+
+Reporting thresholds control which hits are reported in output files (the main
+output, --tblout, and --domtblout).
+
+**E-value (-E)**
+
+In the per-target output, report target profiles with an E-value of <= <x>. The
+default is 10.0, meaning that on average, about 10 false positives will be
+reported per query, so you can see the top of the noise and decide for yourself
+if it’s really noise.
+
+**Bit score (-T)**
+
+Instead of thresholding per-profile output on E-value, instead report target profiles
+with a bit score of >= <x>.
+
+Options for Inclusion Thresholds
+--------------------------------
+
+Inclusion thresholds are stricter than reporting thresholds. Inclusion
+thresholds control which hits are considered to be reliable enough to be
+included in an output alignment or a subsequent search round. In hmmscan, which
+does not have any alignment output (like hmmsearch or phmmer) nor any iterative
+search steps (like jackhmmer), inclusion thresholds have little effect. They
+only affect what domains get marked as significant (!) or questionable (?) in
+domain output.
+
+**E-value of per target inclusion threshold**
+
+Use an E-value of <= <x> as the per-target inclusion threshold. The default is
+0.01, meaning that on average, about 1 false positive would be expected in
+every 100 searches with different query sequences.
+
+**Bit score of per target inclusion threshold**
+
+Instead of using E-values for setting the inclusion threshold, instead use a
+bit score of >= <x> as the per-target inclusion threshold. It would be unusual
+to use bit score thresholds with hmmscan, because you don’t expect a single
+score threshold to work for different profiles; different profiles have
+slightly different expected score distributions.
+
+]]></token>
+  <token name="@ATTRIBUTION@"><![CDATA[
+
+Attribution
+-----------
+
+This Galaxy tool relies on HMMER3_ from http://hmmer.janelia.org/
+Internally the software is cited as:
+
+::
+
+    # hmmscan :: search sequence(s) against a profile database
+    # HMMER 3.1 (February 2013); http://hmmer.org/
+    # Copyright (C) 2011 Howard Hughes Medical Institute.
+    # Freely distributed under the GNU General Public License (GPLv3).
+    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+The wrappers were written by Eric Rasche and is licensed under Apache2_. The
+documentation is copied from the HMMER3 documentation.
+
+.. _Apache2: http://www.apache.org/licenses/LICENSE-2.0
+.. _HMMER3: http://hmmer.janelia.org/
+
+
+  ]]></token>
+  <token name="@HELP_PRE@"><![CDATA[
+
+What it does
+============
+  ]]></token>
+  <token name="@HELP_PRE_OTH@"><![CDATA[
+Options
+=======
+  ]]></token>
+</macros>