# HG changeset patch
# User iuc
# Date 1630399439 0
# Node ID 405dd85a9408a4caf533f49891a3dc8319f364a1
# Parent ffeedf9b8dce8e14357ad89a9a45b73b7f68c211
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
diff -r ffeedf9b8dce -r 405dd85a9408 hmmbuild.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hmmbuild.xml.orig Tue Aug 31 08:43:59 2021 +0000
@@ -0,0 +1,114 @@
+
+<<<<<<< HEAD
+
+ Build a profile HMM from an input multiple alignment
+
+ macros.xml
+
+
+
+
+ Build a profile HMM from an input multiple alignment
+
+
+ macros.xml
+
+
+
+ >>>>>> c37d72558 (add more bio.tool IDs)
+hmmbuild
+
+#if $hmmname:
+ -n '$hmmname'
+#end if
+
+@FORMAT_SELECTOR@
+@MCSS@
+@ARSWS@
+@AEEWS@
+@PRIOR@
+@HSSI@
+@EVAL_CALIB@
+
+@CPU@
+@SEED@
+
+@LENGTHS@
+#if str($maxinsertlen):
+ --maxinsertlen $maxinsertlen
+#end if
+
+'$hmmout'
+'$msafile'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ build a profile HMM and save
+it to a new file .
+
+@HELP_PRE_OTH@
+
+@FORMAT_SELECTOR_HELP@
+@MCSS_HELP@
+@ARSWS_HELP@
+@AEEWS_HELP@
+@PRIOR_HELP@
+@HSSI_HELP@
+@EVAL_CALIB_HELP@
+@SEED_HELP@
+@LENGTHS_HELP@
+
+@ATTRIBUTION@
+ ]]>
+
+
diff -r ffeedf9b8dce -r 405dd85a9408 hmmscan.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hmmscan.xml.orig Tue Aug 31 08:43:59 2021 +0000
@@ -0,0 +1,93 @@
+
+<<<<<<< HEAD
+
+ search protein sequence(s) against a protein profile database
+
+ macros.xml
+
+
+
+
+ search protein sequence(s) against a protein profile database
+
+
+ macros.xml
+
+
+
+ >>>>>> c37d72558 (add more bio.tool IDs)
+@INPUTHMMCHOICE@
+hmmscan
+
+@OFORMAT_WITH_OPTS@
+@THRESHOLDS@
+@CUT@
+@ACCEL_HEUR@
+@ADV_OPTS@
+@CPU@
+@SEED@
+
+'$input_hmm_filename'
+'$seqfile'
+> '$output'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ , use that query sequence to search the
+target database of profiles in , and output ranked lists of the profiles
+with the most significant matches to the sequence.
+
+@HELP_PRE_OTH@
+
+@OFORMAT_WITH_OPTS_HELP@
+@THRESHOLDS_HELP@
+@CUT_HELP@
+@ACCEL_HEUR_HELP@
+@ADV_OPTS_HELP@
+@SEED_HELP@
+
+@ATTRIBUTION@
+ ]]>
+
+
diff -r ffeedf9b8dce -r 405dd85a9408 hmmsearch.xml
--- a/hmmsearch.xml Wed Jul 21 14:06:36 2021 +0000
+++ b/hmmsearch.xml Tue Aug 31 08:43:59 2021 +0000
@@ -1,6 +1,7 @@
search profile(s) against a sequence database
+ macros.xml
diff -r ffeedf9b8dce -r 405dd85a9408 hmmsearch.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hmmsearch.xml.orig Tue Aug 31 08:43:59 2021 +0000
@@ -0,0 +1,102 @@
+
+<<<<<<< HEAD
+
+ search profile(s) against a sequence database
+
+ macros.xml
+
+
+
+
+ search profile(s) against a sequence database
+
+
+ macros.xml
+
+
+
+ >>>>>> c37d72558 (add more bio.tool IDs)
+hmmsearch
+
+@OFORMAT_WITH_OPTS@
+@THRESHOLDS@
+@CUT@
+@ACCEL_HEUR@
+@ADV_OPTS@
+@CPU@
+@SEED@
+
+'$hmmfile'
+'$seqdb'
+> '$output'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ , use that query profile to search the target
+database of sequences in , and output ranked lists of the sequences with
+the most significant matches to the profile. To build profiles from multiple
+alignments, see hmmbuild.
+
+@HELP_PRE_OTH@
+
+@OFORMAT_WITH_OPTS_HELP@
+@THRESHOLDS_HELP@
+@CUT_HELP@
+@ACCEL_HEUR_HELP@
+@ADV_OPTS_HELP@
+@SEED_HELP@
+
+@ATTRIBUTION@
+ ]]>
+
+
diff -r ffeedf9b8dce -r 405dd85a9408 jackhmmer.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/jackhmmer.xml.orig Tue Aug 31 08:43:59 2021 +0000
@@ -0,0 +1,116 @@
+
+<<<<<<< HEAD
+
+ iteratively search a protein sequence against a protein database (PSIBLAST-like)
+
+ macros.xml
+
+
+
+
+ iteratively search a protein sequence against a protein database (PSIBLAST-like)
+
+
+ macros.xml
+
+
+
+ >>>>>> c37d72558 (add more bio.tool IDs)
+jackhmmer
+-N $N
+@OFORMAT_WITH_OPTS@
+@HSSI@
+@THRESHOLDS@
+@ACCEL_HEUR@
+@ARSWS@
+@AEEWS@
+@PRIOR@
+
+@EVAL_CALIB@
+@ADV_OPTS@
+@CPU@
+@SEED@
+
+'$seqfile'
+'$seqdb'
+> '$output'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ against the
+target sequence(s) in . The first iteration is identical to a phmmer
+search. For the next iteration, a multiple alignment of the query together
+with all target sequences satisfying inclusion thresholds is assembled, a
+profile is constructed from this alignment (identical to using hmmbuild on the
+alignment), and profile search of the is done (identical to an
+hmmsearch with the profile).
+
+
+@HELP_PRE_OTH@
+
+@OFORMAT_WITH_OPTS_HELP_NOPFAM@
+@HSSI_HELP@
+@THRESHOLDS_HELP@
+@ACCEL_HEUR_HELP@
+@ARSWS_HELP@
+@AEEWS_HELP@
+@PRIOR_HELP@
+@EVAL_CALIB_HELP@
+@ADV_OPTS_HELP@
+@SEED_HELP@
+
+@ATTRIBUTION@
+ ]]>
+
+
diff -r ffeedf9b8dce -r 405dd85a9408 macros.xml
--- a/macros.xml Wed Jul 21 14:06:36 2021 +0000
+++ b/macros.xml Tue Aug 31 08:43:59 2021 +0000
@@ -6,6 +6,11 @@
+
+
+ hmmer3
+
+ 3.3.2
diff -r ffeedf9b8dce -r 405dd85a9408 macros.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml.orig Tue Aug 31 08:43:59 2021 +0000
@@ -0,0 +1,1126 @@
+
+
+
+
+ hmmer
+
+
+
+<<<<<<< HEAD
+
+
+ gemini
+
+
+=======
+
+
+ hmmer3
+
+
+>>>>>>> 5f65381bd (fix id of hmmer3)
+ 3.3.2
+
+
+
+
+
+
+
+
+
+
+
+-E $E
+--domE $domE
+
+#if str($T):
+ -T $T
+#end if
+
+#if str($domT):
+ --domT $domT
+#end if
+
+#if str($incE):
+ --incE $incE
+#end if
+
+#if str($incdomE):
+ --incdomE $incdomE
+#end if
+
+#if str($incT):
+ --incT $incT
+#end if
+
+#if str($incdomT):
+ --incdomT $incdomT
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+-E $E
+
+#if str($T):
+ -T $T
+#end if
+
+#if str($incE):
+ --incE $incE
+#end if
+
+#if str($incT):
+ --incT $incT
+#end if
+
+
+
+
+
+
+
+
+
+
+$max
+--F1 $F1
+--F2 $F2
+--F3 $F3
+$nobias
+
+
+
+
+
+
+
+
+
+
+--EmL $EmL
+--EmN $EmN
+--EvL $EvL
+--EvN $EvN
+--EfL $EfL
+--EfN $EfN
+--Eft $Eft
+
+
+
+
+
+
+
+
+
+
+
+
+#if $oformat:
+ #for o in str($oformat).split(','):
+ --$o '$getVar($o, 'MISSING_OUTPUT'+$o)'
+ #end for
+#end if
+$acc $noali $notextw
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ oformat and 'tblout' in oformat
+
+
+
+
+
+
+ oformat and 'domtblout' in oformat
+
+
+
+
+
+
+
+ oformat and 'pfamtblout' in oformat
+
+
+
+
+
+
+ oformat and 'dfamtblout' in oformat
+
+
+ oformat and 'aliscoresout' in oformat
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+#if $hssi.hssi_select == "singlemx":
+ --popen $hssi.popen
+ --pextend $hssi.pextend
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ --cpu \$addthreads
+
+
+ --seed $seed
+
+
+
+
+
+
+
+
+$nonull2
+
+#if str($Z):
+ -Z $Z
+#end if
+
+#if str($domZ):
+ --domZ $domZ
+#end if
+
+
+
+
+
+
+
+
+ $input_format_select
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+$arsws.arsws_select
+
+#if $arsws.arsws_select == "--wblosum":
+ --wid $arsws.wid
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+#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 $aeews.eid
+ #end if
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+$cut_ga
+$cut_nc
+$cut_tc
+
+
+
+
+
+
+
+--$mcs.model_construction_strategy_select
+
+#if $mcs.model_construction_strategy_select == "fast":
+ --symfrac $mcs.symfrac
+#end if
+#if str($fragthresh)
+ --fragthresh $fragthresh
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+$aps_select
+
+
+
+
+
+
+
+
+
+
+ 10.1093/nar/gkr367
+
+
+
+#if str($w_beta):
+ --w_beta $w_beta
+#end if
+
+#if str($w_length):
+ --w_length $w_length
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 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 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 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 `__.
+The information posted there may be useful to those who are struggling with
+poor-scoring sequences.
+]]>
+ , 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 , for the
+purposes of per-sequence E-value calculations, rather than the actual number of
+targets seen.
+]]>
+ .
+
+**--ere**
+
+Set the minimum relative entropy/position target to . 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.
+]]>
+
+
+ and the per-domain threshold These act as if
+-T --incT --domT --incdomT 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.
+]]>
+
+
+
+
+**Gap Extend (--pextend)**
+
+Set the gap extend probability for a single sequence query model to .
+
+
+**--mx/--mxfile**
+
+These options are not currently supported
+]]>
+ = W is less than . 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).
+
+]]>
+ = 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 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.
+
+]]>
+
+
+
+
+ , an integer >= 0. If is nonzero,
+any stochastic simulations will be reproducible; the same command will give the
+same results. If is 0, the random number generator is seeded arbitrarily,
+and stochastic simulations will vary from run to run of the same command.
+
+]]>
+ . 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 >= .
+
+**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 <= . 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 >= .
+
+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 <= 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 >= 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 <= 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 >= as the per-domain
+inclusion threshold. As with --incT above, it would be unusual to use a single
+bit score threshold in hmmscan.
+
+]]>
+ . 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 >= .
+
+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 <= 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 >= 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.
+
+]]>
+
+
+
+
diff -r ffeedf9b8dce -r 405dd85a9408 nhmmer.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/nhmmer.xml.orig Tue Aug 31 08:43:59 2021 +0000
@@ -0,0 +1,115 @@
+
+<<<<<<< HEAD
+
+ search a DNA model or alignment against a DNA database (BLASTN-like)
+
+ macros.xml
+
+
+
+
+ search a DNA model or alignment against a DNA database (BLASTN-like)
+
+
+ macros.xml
+
+
+
+ >>>>>> c37d72558 (add more bio.tool IDs)
+nhmmer
+
+@OFORMAT_WITH_OPTS@
+@HSSI@
+@THRESHOLDS_NODOM@
+@CUT@
+@ACCEL_HEUR@
+@FORMAT_SELECTOR@
+@ADV_OPTS@
+@LENGTHS@
+@CPU@
+@SEED@
+
+'$hmmfile'
+'$seqfile'
+> '$output'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ , use that query to search the
+target database of sequences in , and output a ranked list of the hits
+with the most significant matches to the query. A query may be either a profile
+model built using hmmbuild, a sequence alignment, or a single sequence.
+Sequence based queries can be in a number of formats (see --qformat), and can
+typically be autodetected. Note that only Stockholm format supports the use of
+multiple sequence-based queries.
+
+@HELP_PRE_OTH@
+
+@OFORMAT_WITH_OPTS_N_HELP@
+@HSSI_HELP@
+@THRESHOLDS_NODOM_HELP@
+@CUT_HELP@
+@ACCEL_HEUR_HELP@
+@FORMAT_SELECTOR_HELP@
+@ADV_OPTS_HELP@
+@LENGTHS_HELP@
+@SEED_HELP@
+
+@ATTRIBUTION@
+ ]]>
+
+
diff -r ffeedf9b8dce -r 405dd85a9408 nhmmscan.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/nhmmscan.xml.orig Tue Aug 31 08:43:59 2021 +0000
@@ -0,0 +1,113 @@
+
+<<<<<<< HEAD
+
+ search DNA sequence(s) against a DNA profile database
+
+ macros.xml
+
+
+
+
+ search DNA sequence(s) against a DNA profile database
+
+
+ macros.xml
+
+
+
+ >>>>>> c37d72558 (add more bio.tool IDs)
+@INPUTHMMCHOICE@
+nhmmscan
+
+@OFORMAT_WITH_OPTS@
+@THRESHOLDS_NODOM@
+@CUT@
+@ACCEL_HEUR@
+--B1 $B1
+--B2 $B2
+--B3 $B3
+
+@ADV_OPTS@
+@LENGTHS@
+@CPU@
+@SEED@
+
+'$input_hmm_filename'
+'$seqfile'
+> '$output'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ , use that query sequence to
+search the target database of profiles in , and output ranked lists of
+the profiles with the most significant matches to the sequence.
+
+The may contain more than one query sequence. It can be in FASTA
+format, or several other common sequence file formats (genbank, embl, and
+uniprot, among others), or in alignment file formats (stockholm, aligned fasta,
+and others). See the --qformat option for a complete list.
+
+@HELP_PRE_OTH@
+
+@OFORMAT_WITH_OPTS_N_HELP@
+@THRESHOLDS_NODOM_HELP@
+@CUT_HELP@
+@ACCEL_HEUR_HELP@
+@BIAS_COMP_HELP@
+@ADV_OPTS_HELP@
+@LENGTHS_HELP@
+@SEED_HELP@
+
+
+@ATTRIBUTION@
+]]>
+
+
diff -r ffeedf9b8dce -r 405dd85a9408 phmmer.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phmmer.xml.orig Tue Aug 31 08:43:59 2021 +0000
@@ -0,0 +1,107 @@
+
+<<<<<<< HEAD
+
+ search a protein sequence against a protein database (BLASTP-like)
+
+ macros.xml
+
+
+
+
+ search a protein sequence against a protein database (BLASTP-like)
+
+
+ macros.xml
+
+
+
+ >>>>>> c37d72558 (add more bio.tool IDs)
+phmmer
+
+@OFORMAT_WITH_OPTS@
+@HSSI@
+@THRESHOLDS@
+@ACCEL_HEUR@
+@EVAL_CALIB@
+@ADV_OPTS@
+
+@CPU@
+@SEED@
+
+'$seqfile'
+'$seqdb'
+> '$output'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ , use that sequence to
+search the target database of sequences in , and output ranked lists of
+the sequences with the most significant matches to the query.
+
+
+@HELP_PRE_OTH@
+
+@OFORMAT_WITH_OPTS_HELP@
+@HSSI_HELP@
+@THRESHOLDS_HELP@
+@ACCEL_HEUR_HELP@
+@EVAL_CALIB_HELP@
+@ADV_OPTS_HELP@
+@SEED_HELP@
+
+@ATTRIBUTION@
+ ]]>
+
+