Mercurial > repos > iuc > hmmer_jackhmmer
diff macros.xml @ 3:036df14999e8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
| author | iuc |
|---|---|
| date | Sat, 07 Apr 2018 03:48:57 -0400 |
| parents | 4e0cbf379bab |
| children | 793967b6ae8a |
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--- a/macros.xml Wed Apr 04 14:00:07 2018 -0400 +++ b/macros.xml Sat Apr 07 03:48:57 2018 -0400 @@ -2,11 +2,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="3.1b2">hmmer</requirement> + <requirement type="package" version="@TOOL_VERSION@">hmmer</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">0.1</token> + <token name="@TOOL_VERSION@">3.1b2</token> <xml name="stdio"> <stdio> <!-- Anything other than zero is an error --> @@ -21,64 +21,64 @@ -E $E --domE $domE -#if $T: --T $T +#if str($T): + -T $T #end if -#if $domT: ---domT $domT +#if str($domT): + --domT $domT #end if -#if $incE: ---incE $incE +#if str($incE): + --incE $incE #end if -#if $incT: ---incT $incT +#if str($incdomE): + --incdomE $incdomE #end if -#if $incdomE: ---incdomE $incdomE +#if str($incT): + --incT $incT #end if -#if $incdomT: ---incdomT $incdomT +#if str($incdomT): + --incdomT $incdomT #end if </token> <xml name="thresholds_xml"> <!-- Options controlling reporting thresholds --> - <param name="E" label="report sequences <= this E-Value threshold in output" help="(-E)" value="10.0" type="float" min="0"/> - <param name="domE" label="report domains <= this E-Value threshold in output" help="(--domE)" value="10.0" type="float" min="0"/> - <param name="T" label="report sequences >= this score threshold in output" help="(-T)" type="float" optional="True"/> - <param name="domT" label="report domains >= this score threshold in output" help="(--domT)" type="float" optional="True"/> + <param argument="-E" type="float" min="0" value="10.0" label="report sequences <= this E-Value threshold in output" /> + <param argument="--domE" type="float" min="0" value="10.0" label="report domains <= this E-Value threshold in output" /> + <param argument="-T" type="float" optional="true" label="report sequences >= this score threshold in output" /> + <param argument="--domT" type="float" optional="true" label="report domains >= this score threshold in output" /> <!-- Options controlling inclusion (significance) thresholds --> - <param name="incE" label="consider sequences <= this E-Value threshold as significant" help="(--incE)" type="float" optional="True"/> - <param name="incdomE" label="consider domains <= this E-Value threshold as significant" help="(--incdomE)" type="float" optional="True"/> - <param name="incT" label="consider sequences >= this score threshold as significant" help="(--incT)" type="float" optional="True"/> - <param name="incdomT" label="consider domains >= this score threshold as significant" help="(--incdomT)" type="float" optional="True"/> + <param argument="--incE" type="float" optional="true" label="consider sequences <= this E-Value threshold as significant" /> + <param argument="--incdomE" type="float" optional="true" label="consider domains <= this E-Value threshold as significant" /> + <param argument="--incT" type="float" optional="true" label="consider sequences >= this score threshold as significant" /> + <param argument="--incdomT" type="float" optional="true" label="consider domains >= this score threshold as significant" /> </xml> <token name="@THRESHOLDS_NODOM@"> -E $E -#if $T: --T $T +#if str($T): + -T $T #end if -#if $incE: ---incE $incE +#if str($incE): + --incE $incE #end if -#if $incT: ---incT $incT +#if str($incT): + --incT $incT #end if </token> <xml name="thresholds_nodom"> <!-- Options controlling reporting thresholds --> - <param name="E" label="report sequences <= this E-Value threshold in output" help="(-E)" value="10.0" type="float" min="0"/> - <param name="T" label="report sequences >= this score threshold in output" help="(-T)" type="float" optional="True"/> + <param argument="-E" type="float" min="0" value="10.0" label="report sequences <= this E-Value threshold in output" /> + <param argument="-T" type="float" optional="true" label="report sequences >= this score threshold in output" /> <!-- Options controlling inclusion (significance) thresholds --> - <param name="incE" label="consider sequences <= this E-Value threshold as significant" help="(--incE)" type="float" optional="True"/> - <param name="incT" label="consider sequences >= this score threshold as significant" help="(--incT)" type="float" optional="True"/> + <param argument="--incE" type="float" optional="true" label="consider sequences <= this E-Value threshold as significant" /> + <param argument="--incT" type="float" optional="true" label="consider sequences >= this score threshold as significant" /> </xml> <token name="@ACCEL_HEUR@"> $max @@ -86,15 +86,14 @@ --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 <= F1" help="(--F1)" value="0.02"/> - <param name="F2" type="float" label="Stage 2 (Vit) threshold: promote hits w/ P <= F2" help="(--F2)" value="1e-3"/> - <param name="F3" type="float" label="Stage 3 (Fwd) threshold: promote hits w/ P <= F3" help="(--F3)" value="1e-5"/> - <param name="nobias" type="boolean" truevalue="--nobias" label="Turn off composition bias filter" help="(--nobias)" falsevalue=""/> + <param argument="--max" type="boolean" truevalue="--max" falsevalue="" label="Turn all heuristic filters off (less speed, more power)" /> + <param argument="--F1" type="float" value="0.02" label="Stage 1 (MSV) threshold: promote hits w/ P <= F1" /> + <param argument="--F2" type="float" value="1e-3" label="Stage 2 (Vit) threshold: promote hits w/ P <= F2" /> + <param argument="--F3" type="float" value="1e-5" label="Stage 3 (Fwd) threshold: promote hits w/ P <= F3" /> + <param argument="--nobias" type="boolean" truevalue="--nobias" falsevalue="" label="Turn off composition bias filter" /> </xml> <token name="@EVAL_CALIB@"> --EmL $EmL @@ -107,90 +106,90 @@ </token> <xml name="eval_calib_xml"> <!-- Control of E-value calibration --> - <param name="EmL" type="integer" value="200" min="1" help="(--EmL)" label="Length of sequences for MSV Gumbel mu fit"/> - <param name="EmN" type="integer" value="200" min="1" help="(--EmN)" label="Number of sequences for MSV Gumbel mu fit"/> - <param name="EvL" type="integer" value="200" min="1" help="(--EvL)" label="Length of sequences for Viterbi Gumbel mu fit"/> - <param name="EvN" type="integer" value="200" min="1" help="(--EvN)" label="Number of sequences for Viterbi Gumbel mu fit"/> - <param name="EfL" type="integer" value="100" min="1" help="(--EfL)" label="Length of sequences for Forward exp tail tau fit"/> - <param name="EfN" type="integer" value="200" min="1" help="(--EfN)" label="Number of sequences for Forward exp tail tau fit"/> - <param name="Eft" type="float" value="0.04" min="0" max="1" help="(--Eft)" label="tail mass for Forward exponential tail tau fit"/> + <param argument="--EmL" type="integer" min="1" value="200" label="Length of sequences for MSV Gumbel mu fit" /> + <param argument="--EmN" type="integer" min="1" value="200" label="Number of sequences for MSV Gumbel mu fit" /> + <param argument="--EvL" type="integer" min="1" value="200" label="Length of sequences for Viterbi Gumbel mu fit" /> + <param argument="--EvN" type="integer" min="1" value="200" label="Number of sequences for Viterbi Gumbel mu fit" /> + <param argument="--EfL" type="integer" min="1" value="100" label="Length of sequences for Forward exp tail tau fit" /> + <param argument="--EfN" type="integer" min="1" value="200" label="Number of sequences for Forward exp tail tau fit" /> + <param argument="--Eft" type="float" min="0" max="1" value="0.04" label="tail mass for Forward exponential tail tau fit" /> </xml> <token name="@OFORMAT_WITH_OPTS_NOPFAM@"> #if 'tblout' in str($oformat): - --tblout $tblout + --tblout '$tblout' #end if #if 'domtblout' in str($oformat): - --domtblout $domtblout + --domtblout '$domtblout' #end if $acc $noali $notextw </token> <xml name="oformat_with_opts_nopfam"> <!-- Options directing output --> - <param name="oformat" multiple="True" display="checkboxes" label="Output Formats" type="select"> + <param name="oformat" multiple="true" display="checkboxes" label="Output Formats" type="select"> <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option> <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option> </param> - <param name="acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" help="(--acc)"/> - <param name="noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" help="(--noali)"/> - <param name="notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" help="(--notextw)"/> + <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" /> + <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" /> + <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" /> </xml> <token name="@OFORMAT_WITH_OPTS@"> #if 'tblout' in str($oformat): - --tblout $tblout + --tblout '$tblout' #end if #if 'domtblout' in str($oformat): - --domtblout $domtblout + --domtblout '$domtblout' #end if #if 'pfamtblout' in str($oformat): - --pfamtblout $pfamtblout + --pfamtblout '$pfamtblout' #end if $acc $noali $notextw </token> <xml name="oformat_with_opts"> <!-- Options directing output --> - <param name="oformat" multiple="True" display="checkboxes" label="Output Formats" type="select"> + <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats"> <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option> <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option> <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option> </param> - <param name="acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" help="(--acc)"/> - <param name="noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" help="(--noali)"/> - <param name="notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" help="(--notextw)"/> + <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" /> + <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" /> + <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" /> </xml> <xml name="oformat_test"> - <param name="notextw" value="True" /> + <param name="notextw" value="true" /> </xml> <!-- TODO: tblout will match 'pfamtblout,dfamtblout' --> <token name="@OFORMAT_WITH_OPTS_N@"> #if 'tblout' in str($oformat): - --tblout $tblout + --tblout '$tblout' #end if #if 'dfamtblout' in str($oformat): - --dfamtblout $dfamtblout + --dfamtblout '$dfamtblout' #end if #if 'aliscoresout' in str($oformat): - --aliscoresout $aliscoresout + --aliscoresout '$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"> + <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats"> <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)"/> + <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" /> + <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" /> + <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" /> </xml> <token name="@HSSI@"> #if $hssi.hssi_select == "singlemx": @@ -205,11 +204,10 @@ <option value="false" selected="true">Disable</option> <option value="singlemx">Use substitution score matrix for single-sequence inputs</option> </param> + <when value="false" /> <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"> + <param argument="--popen" type="float" min="0.0" max="0.5" value="0.02" label="Gap open probability" /> + <param argument="--pextend" type="float" min="0.0" max="1.0" value="0.4" label="Gap extend probability" /> </when> <!-- -mx <s> : substitution score matrix (built-in matrices, with -singlemx)--> <!-- -mxfile <f> : read substitution score matrix from file <f> (with -singlemx)--> @@ -222,7 +220,7 @@ --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"/> + <param argument="--seed" type="integer" min="0" value="42" label="RNG seed, 0 generates a random seed" /> </xml> <xml name="seed_test"> <param name="seed" value="4" /> @@ -230,19 +228,19 @@ <token name="@ADV_OPTS@"> $nonull2 -#if $Z: --Z $Z +#if str($Z): + -Z $Z #end if -#if $domZ: ---domZ $domZ +#if str($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"/> + <param argument="--nonull2" type="boolean" truevalue="--nonull2" falsevalue="" label="Turn off biased composition score corrections" /> + <param argument="-Z" type="integer" optional="true" label="# of comparisons done for E-value calculation" /> + <param argument="--domZ" type="integer" optional="true" label="# of significant sequences, for domain E-value calculation" /> </xml> <token name="@FORMAT_SELECTOR@"> $input_format_select @@ -264,7 +262,7 @@ $arsws.arsws_select #if $arsws.arsws_select == "--wblosum": ---wid $arsws.wid + --wid $arsws.wid #end if </token> <xml name="arsws"> @@ -282,7 +280,7 @@ <when value="--wgsc"> </when> <when value="--wblosum"> - <param name="wid" label="Set identity cutoff" value="0.62" type="float" help="(--wid)"/> + <param argument="--wid" type="float" value="0.62" label="Set identity cutoff" /> </when> <when value="--wnone"> </when> @@ -315,13 +313,13 @@ <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)"/> + <param argument="--eset" type="float" value="0" label="set eff seq # for all models" /> + <param argument="--ere" type="float" value="0" label="set minimum rel entropy/position" /> + <param argument="--esigma" type="float" value="45" label="set sigma param" /> </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)"/> + <param argument="--eset" type="float" value="0" label="set eff seq # for all models" /> + <param argument="--eid" type="float" min="0" max="1" value="0.62" label="set fractional identity cutoff" /> </when> <when value="enone"> </when> @@ -333,17 +331,19 @@ $cut_tc </token> <xml name="cut"> - <param name="cut_ga" type="boolean" truevalue="--cut_ga" label="use profile's GA gathering cutoffs to set all thresholding" help="(--cut_ga)" falsevalue=""/> - <param name="cut_nc" type="boolean" truevalue="--cut_nc" label="use profile's NC gathering cutoffs to set all thresholding" help="(--cut_nc)" falsevalue=""/> - <param name="cut_tc" type="boolean" truevalue="--cut_tc" label="use profile's TC gathering cutoffs to set all thresholding" help="(--cut_tc)" falsevalue=""/> + <param argument="--cut_ga" type="boolean" truevalue="--cut_ga" falsevalue="" label="use profile's GA gathering cutoffs to set all thresholding" /> + <param argument="--cut_nc" type="boolean" truevalue="--cut_nc" falsevalue="" label="use profile's NC gathering cutoffs to set all thresholding" /> + <param argument="--cut_tc" type="boolean" truevalue="--cut_tc" falsevalue="" label="use profile's TC gathering cutoffs to set all thresholding" /> </xml> <token name="@MCSS@"> --$mcs.model_construction_strategy_select #if $mcs.model_construction_strategy_select == "fast": ---symfrac $mcs.symfrac + --symfrac $mcs.symfrac #end if - +#if str($fragthresh) + --fragthresh $fragthresh +#end if </token> <xml name="mcss"> <!-- Alternative model construction strategies --> @@ -353,12 +353,11 @@ <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"/> + <param argument="--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" /> - + <param argument="--fragthresh" type="float" value="0.5" optional="true" 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" /> </xml> <token name="@PRIOR@"> $aps_select @@ -376,32 +375,32 @@ </citations> </xml> <token name="@LENGTHS@"> -#if $w_beta: ---w_beta $w_beta +#if str($w_beta): + --w_beta $w_beta #end if -#if $w_length: ---w_length $w_length +#if str($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" /> + <param argument="--w_beta" type="float" optional="true" label="Tail mass at which window length is determined" /> + <param argument="--w_length" type="integer" optional="true" label="Window Length" /> </xml> - <token name="@INPUTHMMCHOICE@"> + <token name="@INPUTHMMCHOICE@"><![CDATA[ #if $input_hmm_conditional.input_hmm_source == "history": - '$input_hmm_conditional.hmmfile' + #set $input_hmm_filename = "localref.hmm" + ln -s '${input_hmm_conditional.hmmfile}' '${input_hmm_filename}' && + ## "Press" database + hmmpress '${input_hmm_filename}' && #else: - '$input_hmm_conditional.index.fields.db_path' + #set $input_hmm_filename = str($input_hmm_conditional.index.fields.db_path) #end if - </token> + ]]></token> <xml name="input_hmm_choice"> <conditional name="input_hmm_conditional"> <param name="input_hmm_source" type="select" label="Use a built-in HMM model database or own from your history" > - <option value="indexed" selected="True">Use a built-in HMM model database</option> + <option value="indexed" selected="true">Use a built-in HMM model database</option> <option value="history">Use a HMM database from history</option> </param> <when value="indexed"> @@ -413,12 +412,12 @@ </param> </when> <when value="history"> - <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/> + <param name="hmmfile" type="data" format="hmm2,hmm3" label="HMM model" /> </when> <!-- history --> </conditional> <!-- input_hmm_conditional --> </xml> <xml name="input_hmm"> - <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/> + <param name="hmmfile" type="data" format="hmm2,hmm3" label="HMM model" /> </xml> <xml name="input_msa"> <param name="msafile" type="data" label="Multiple Sequence Alignment" format="stockholm,clustal,fasta"