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comparison macros.xml @ 5:11c9fd078fbd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
author iuc
date Sat, 07 Apr 2018 03:44:11 -0400
parents 8d17f2095928
children 534dfce4cd86
comparison
equal deleted inserted replaced
4:b712a9f5d3fe 5:11c9fd078fbd
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.1b2">hmmer</requirement> 5 <requirement type="package" version="@TOOL_VERSION@">hmmer</requirement>
6 <yield/> 6 <yield/>
7 </requirements> 7 </requirements>
8 </xml> 8 </xml>
9 <token name="@WRAPPER_VERSION@">0.1</token> 9 <token name="@TOOL_VERSION@">3.1b2</token>
10 <xml name="stdio"> 10 <xml name="stdio">
11 <stdio> 11 <stdio>
12 <!-- Anything other than zero is an error --> 12 <!-- Anything other than zero is an error -->
13 <exit_code range="1:"/> 13 <exit_code range="1:"/>
14 <exit_code range=":-1"/> 14 <exit_code range=":-1"/>
19 </xml> 19 </xml>
20 <token name="@THRESHOLDS@"> 20 <token name="@THRESHOLDS@">
21 -E $E 21 -E $E
22 --domE $domE 22 --domE $domE
23 23
24 #if $T: 24 #if str($T):
25 -T $T 25 -T $T
26 #end if 26 #end if
27 27
28 #if $domT: 28 #if str($domT):
29 --domT $domT 29 --domT $domT
30 #end if 30 #end if
31 31
32 #if $incE: 32 #if str($incE):
33 --incE $incE 33 --incE $incE
34 #end if 34 #end if
35 35
36 #if $incT: 36 #if str($incdomE):
37 --incT $incT 37 --incdomE $incdomE
38 #end if 38 #end if
39 39
40 #if $incdomE: 40 #if str($incT):
41 --incdomE $incdomE 41 --incT $incT
42 #end if 42 #end if
43 43
44 #if $incdomT: 44 #if str($incdomT):
45 --incdomT $incdomT 45 --incdomT $incdomT
46 #end if 46 #end if
47 </token> 47 </token>
48 <xml name="thresholds_xml"> 48 <xml name="thresholds_xml">
49 <!-- Options controlling reporting thresholds --> 49 <!-- Options controlling reporting thresholds -->
50 <param name="E" label="report sequences &lt;= this E-Value threshold in output" help="(-E)" value="10.0" type="float" min="0"/> 50 <param argument="-E" type="float" min="0" value="10.0" label="report sequences &lt;= this E-Value threshold in output" />
51 <param name="domE" label="report domains &lt;= this E-Value threshold in output" help="(--domE)" value="10.0" type="float" min="0"/> 51 <param argument="--domE" type="float" min="0" value="10.0" label="report domains &lt;= this E-Value threshold in output" />
52 <param name="T" label="report sequences &gt;= this score threshold in output" help="(-T)" type="float" optional="True"/> 52 <param argument="-T" type="float" optional="true" label="report sequences &gt;= this score threshold in output" />
53 <param name="domT" label="report domains &gt;= this score threshold in output" help="(--domT)" type="float" optional="True"/> 53 <param argument="--domT" type="float" optional="true" label="report domains &gt;= this score threshold in output" />
54 <!-- Options controlling inclusion (significance) thresholds --> 54 <!-- Options controlling inclusion (significance) thresholds -->
55 <param name="incE" label="consider sequences &lt;= this E-Value threshold as significant" help="(--incE)" type="float" optional="True"/> 55 <param argument="--incE" type="float" optional="true" label="consider sequences &lt;= this E-Value threshold as significant" />
56 <param name="incdomE" label="consider domains &lt;= this E-Value threshold as significant" help="(--incdomE)" type="float" optional="True"/> 56 <param argument="--incdomE" type="float" optional="true" label="consider domains &lt;= this E-Value threshold as significant" />
57 <param name="incT" label="consider sequences &gt;= this score threshold as significant" help="(--incT)" type="float" optional="True"/> 57 <param argument="--incT" type="float" optional="true" label="consider sequences &gt;= this score threshold as significant" />
58 <param name="incdomT" label="consider domains &gt;= this score threshold as significant" help="(--incdomT)" type="float" optional="True"/> 58 <param argument="--incdomT" type="float" optional="true" label="consider domains &gt;= this score threshold as significant" />
59 </xml> 59 </xml>
60 <token name="@THRESHOLDS_NODOM@"> 60 <token name="@THRESHOLDS_NODOM@">
61 -E $E 61 -E $E
62 62
63 #if $T: 63 #if str($T):
64 -T $T 64 -T $T
65 #end if 65 #end if
66 66
67 #if $incE: 67 #if str($incE):
68 --incE $incE 68 --incE $incE
69 #end if 69 #end if
70 70
71 #if $incT: 71 #if str($incT):
72 --incT $incT 72 --incT $incT
73 #end if 73 #end if
74 </token> 74 </token>
75 <xml name="thresholds_nodom"> 75 <xml name="thresholds_nodom">
76 <!-- Options controlling reporting thresholds --> 76 <!-- Options controlling reporting thresholds -->
77 <param name="E" label="report sequences &lt;= this E-Value threshold in output" help="(-E)" value="10.0" type="float" min="0"/> 77 <param argument="-E" type="float" min="0" value="10.0" label="report sequences &lt;= this E-Value threshold in output" />
78 <param name="T" label="report sequences &gt;= this score threshold in output" help="(-T)" type="float" optional="True"/> 78 <param argument="-T" type="float" optional="true" label="report sequences &gt;= this score threshold in output" />
79 <!-- Options controlling inclusion (significance) thresholds --> 79 <!-- Options controlling inclusion (significance) thresholds -->
80 <param name="incE" label="consider sequences &lt;= this E-Value threshold as significant" help="(--incE)" type="float" optional="True"/> 80 <param argument="--incE" type="float" optional="true" label="consider sequences &lt;= this E-Value threshold as significant" />
81 <param name="incT" label="consider sequences &gt;= this score threshold as significant" help="(--incT)" type="float" optional="True"/> 81 <param argument="--incT" type="float" optional="true" label="consider sequences &gt;= this score threshold as significant" />
82 </xml> 82 </xml>
83 <token name="@ACCEL_HEUR@"> 83 <token name="@ACCEL_HEUR@">
84 $max 84 $max
85 --F1 $F1 85 --F1 $F1
86 --F2 $F2 86 --F2 $F2
87 --F3 $F3 87 --F3 $F3
88 $nobias 88 $nobias
89
90 </token> 89 </token>
91 <xml name="accel_heur_xml"> 90 <xml name="accel_heur_xml">
92 <!-- Options controlling acceleration heuristics --> 91 <!-- Options controlling acceleration heuristics -->
93 <param name="max" type="boolean" truevalue="--max" label="Turn all heuristic filters off (less speed, more power)" help="(--max)" falsevalue=""/> 92 <param argument="--max" type="boolean" truevalue="--max" falsevalue="" label="Turn all heuristic filters off (less speed, more power)" />
94 <param name="F1" type="float" label="Stage 1 (MSV) threshold: promote hits w/ P &lt;= F1" help="(--F1)" value="0.02"/> 93 <param argument="--F1" type="float" value="0.02" label="Stage 1 (MSV) threshold: promote hits w/ P &lt;= F1" />
95 <param name="F2" type="float" label="Stage 2 (Vit) threshold: promote hits w/ P &lt;= F2" help="(--F2)" value="1e-3"/> 94 <param argument="--F2" type="float" value="1e-3" label="Stage 2 (Vit) threshold: promote hits w/ P &lt;= F2" />
96 <param name="F3" type="float" label="Stage 3 (Fwd) threshold: promote hits w/ P &lt;= F3" help="(--F3)" value="1e-5"/> 95 <param argument="--F3" type="float" value="1e-5" label="Stage 3 (Fwd) threshold: promote hits w/ P &lt;= F3" />
97 <param name="nobias" type="boolean" truevalue="--nobias" label="Turn off composition bias filter" help="(--nobias)" falsevalue=""/> 96 <param argument="--nobias" type="boolean" truevalue="--nobias" falsevalue="" label="Turn off composition bias filter" />
98 </xml> 97 </xml>
99 <token name="@EVAL_CALIB@"> 98 <token name="@EVAL_CALIB@">
100 --EmL $EmL 99 --EmL $EmL
101 --EmN $EmN 100 --EmN $EmN
102 --EvL $EvL 101 --EvL $EvL
105 --EfN $EfN 104 --EfN $EfN
106 --Eft $Eft 105 --Eft $Eft
107 </token> 106 </token>
108 <xml name="eval_calib_xml"> 107 <xml name="eval_calib_xml">
109 <!-- Control of E-value calibration --> 108 <!-- Control of E-value calibration -->
110 <param name="EmL" type="integer" value="200" min="1" help="(--EmL)" label="Length of sequences for MSV Gumbel mu fit"/> 109 <param argument="--EmL" type="integer" min="1" value="200" label="Length of sequences for MSV Gumbel mu fit" />
111 <param name="EmN" type="integer" value="200" min="1" help="(--EmN)" label="Number of sequences for MSV Gumbel mu fit"/> 110 <param argument="--EmN" type="integer" min="1" value="200" label="Number of sequences for MSV Gumbel mu fit" />
112 <param name="EvL" type="integer" value="200" min="1" help="(--EvL)" label="Length of sequences for Viterbi Gumbel mu fit"/> 111 <param argument="--EvL" type="integer" min="1" value="200" label="Length of sequences for Viterbi Gumbel mu fit" />
113 <param name="EvN" type="integer" value="200" min="1" help="(--EvN)" label="Number of sequences for Viterbi Gumbel mu fit"/> 112 <param argument="--EvN" type="integer" min="1" value="200" label="Number of sequences for Viterbi Gumbel mu fit" />
114 <param name="EfL" type="integer" value="100" min="1" help="(--EfL)" label="Length of sequences for Forward exp tail tau fit"/> 113 <param argument="--EfL" type="integer" min="1" value="100" label="Length of sequences for Forward exp tail tau fit" />
115 <param name="EfN" type="integer" value="200" min="1" help="(--EfN)" label="Number of sequences for Forward exp tail tau fit"/> 114 <param argument="--EfN" type="integer" min="1" value="200" label="Number of sequences for Forward exp tail tau fit" />
116 <param name="Eft" type="float" value="0.04" min="0" max="1" help="(--Eft)" label="tail mass for Forward exponential tail tau fit"/> 115 <param argument="--Eft" type="float" min="0" max="1" value="0.04" label="tail mass for Forward exponential tail tau fit" />
117 </xml> 116 </xml>
118 <token name="@OFORMAT_WITH_OPTS_NOPFAM@"> 117 <token name="@OFORMAT_WITH_OPTS_NOPFAM@">
119 #if 'tblout' in str($oformat): 118 #if 'tblout' in str($oformat):
120 --tblout $tblout 119 --tblout '$tblout'
121 #end if 120 #end if
122 121
123 #if 'domtblout' in str($oformat): 122 #if 'domtblout' in str($oformat):
124 --domtblout $domtblout 123 --domtblout '$domtblout'
125 #end if 124 #end if
126 125
127 $acc $noali $notextw 126 $acc $noali $notextw
128 </token> 127 </token>
129 <xml name="oformat_with_opts_nopfam"> 128 <xml name="oformat_with_opts_nopfam">
130 <!-- Options directing output --> 129 <!-- Options directing output -->
131 <param name="oformat" multiple="True" display="checkboxes" label="Output Formats" type="select"> 130 <param name="oformat" multiple="true" display="checkboxes" label="Output Formats" type="select">
132 <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option> 131 <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
133 <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option> 132 <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
134 </param> 133 </param>
135 <param name="acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" help="(--acc)"/> 134 <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" />
136 <param name="noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" help="(--noali)"/> 135 <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" />
137 <param name="notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" help="(--notextw)"/> 136 <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" />
138 </xml> 137 </xml>
139 <token name="@OFORMAT_WITH_OPTS@"> 138 <token name="@OFORMAT_WITH_OPTS@">
140 #if 'tblout' in str($oformat): 139 #if 'tblout' in str($oformat):
141 --tblout $tblout 140 --tblout '$tblout'
142 #end if 141 #end if
143 142
144 #if 'domtblout' in str($oformat): 143 #if 'domtblout' in str($oformat):
145 --domtblout $domtblout 144 --domtblout '$domtblout'
146 #end if 145 #end if
147 146
148 #if 'pfamtblout' in str($oformat): 147 #if 'pfamtblout' in str($oformat):
149 --pfamtblout $pfamtblout 148 --pfamtblout '$pfamtblout'
150 #end if 149 #end if
151 150
152 $acc $noali $notextw 151 $acc $noali $notextw
153 </token> 152 </token>
154 <xml name="oformat_with_opts"> 153 <xml name="oformat_with_opts">
155 <!-- Options directing output --> 154 <!-- Options directing output -->
156 <param name="oformat" multiple="True" display="checkboxes" label="Output Formats" type="select"> 155 <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats">
157 <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option> 156 <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
158 <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option> 157 <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
159 <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option> 158 <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option>
160 </param> 159 </param>
161 <param name="acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" help="(--acc)"/> 160 <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" />
162 <param name="noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" help="(--noali)"/> 161 <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" />
163 <param name="notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" help="(--notextw)"/> 162 <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" />
164 </xml> 163 </xml>
165 <xml name="oformat_test"> 164 <xml name="oformat_test">
166 <param name="notextw" value="True" /> 165 <param name="notextw" value="true" />
167 </xml> 166 </xml>
168 <!-- TODO: tblout will match 'pfamtblout,dfamtblout' --> 167 <!-- TODO: tblout will match 'pfamtblout,dfamtblout' -->
169 <token name="@OFORMAT_WITH_OPTS_N@"> 168 <token name="@OFORMAT_WITH_OPTS_N@">
170 #if 'tblout' in str($oformat): 169 #if 'tblout' in str($oformat):
171 --tblout $tblout 170 --tblout '$tblout'
172 #end if 171 #end if
173 172
174 #if 'dfamtblout' in str($oformat): 173 #if 'dfamtblout' in str($oformat):
175 --dfamtblout $dfamtblout 174 --dfamtblout '$dfamtblout'
176 #end if 175 #end if
177 176
178 #if 'aliscoresout' in str($oformat): 177 #if 'aliscoresout' in str($oformat):
179 --aliscoresout $aliscoresout 178 --aliscoresout '$aliscoresout'
180 #end if 179 #end if
181 180
182 $acc $noali $notextw 181 $acc $noali $notextw
183 </token> 182 </token>
184 <xml name="oformat_with_opts_n"> 183 <xml name="oformat_with_opts_n">
185 <!-- Options directing output --> 184 <!-- Options directing output -->
186 <param name="oformat" multiple="True" display="checkboxes" label="Output Formats" type="select"> 185 <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats">
187 <option value="tblout" selected="true">Table of hits (--tblout)</option> 186 <option value="tblout" selected="true">Table of hits (--tblout)</option>
188 <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option> 187 <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option>
189 <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option> 188 <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option>
190 </param> 189 </param>
191 <param name="acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" help="(--acc)"/> 190 <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" />
192 <param name="noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" help="(--noali)"/> 191 <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" />
193 <param name="notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" help="(--notextw)"/> 192 <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" />
194 </xml> 193 </xml>
195 <token name="@HSSI@"> 194 <token name="@HSSI@">
196 #if $hssi.hssi_select == "singlemx": 195 #if $hssi.hssi_select == "singlemx":
197 --popen $hssi.popen 196 --popen $hssi.popen
198 --pextend $hssi.pextend 197 --pextend $hssi.pextend
203 <conditional name="hssi"> 202 <conditional name="hssi">
204 <param name="hssi_select" type="select" label="Options for handling single sequence inputs"> 203 <param name="hssi_select" type="select" label="Options for handling single sequence inputs">
205 <option value="false" selected="true">Disable</option> 204 <option value="false" selected="true">Disable</option>
206 <option value="singlemx">Use substitution score matrix for single-sequence inputs</option> 205 <option value="singlemx">Use substitution score matrix for single-sequence inputs</option>
207 </param> 206 </param>
207 <when value="false" />
208 <when value="singlemx"> 208 <when value="singlemx">
209 <param name="popen" type="float" value="0.02" label="Gap open probability" help="(--popen)" min="0.0" max="0.5"/> 209 <param argument="--popen" type="float" min="0.0" max="0.5" value="0.02" label="Gap open probability" />
210 <param name="pextend" type="float" value="0.4" label="Gap extend probability" help="(--pextend)" min="0.0" max="1.0"/> 210 <param argument="--pextend" type="float" min="0.0" max="1.0" value="0.4" label="Gap extend probability" />
211 </when>
212 <when value="false">
213 </when> 211 </when>
214 <!-- -mx <s> : substitution score matrix (built-in matrices, with -singlemx)--> 212 <!-- -mx <s> : substitution score matrix (built-in matrices, with -singlemx)-->
215 <!-- -mxfile <f> : read substitution score matrix from file <f> (with -singlemx)--> 213 <!-- -mxfile <f> : read substitution score matrix from file <f> (with -singlemx)-->
216 </conditional> 214 </conditional>
217 </xml> 215 </xml>
220 </token> 218 </token>
221 <token name="@SEED@"> 219 <token name="@SEED@">
222 --seed $seed 220 --seed $seed
223 </token> 221 </token>
224 <xml name="seed"> 222 <xml name="seed">
225 <param name="seed" label="RNG seed, 0 generates a random seed" value="42" type="integer" help="(--seed)" min="0"/> 223 <param argument="--seed" type="integer" min="0" value="42" label="RNG seed, 0 generates a random seed" />
226 </xml> 224 </xml>
227 <xml name="seed_test"> 225 <xml name="seed_test">
228 <param name="seed" value="4" /> 226 <param name="seed" value="4" />
229 </xml> 227 </xml>
230 <token name="@ADV_OPTS@"> 228 <token name="@ADV_OPTS@">
231 $nonull2 229 $nonull2
232 230
233 #if $Z: 231 #if str($Z):
234 -Z $Z 232 -Z $Z
235 #end if 233 #end if
236 234
237 #if $domZ: 235 #if str($domZ):
238 --domZ $domZ 236 --domZ $domZ
239 #end if 237 #end if
240 </token> 238 </token>
241 <xml name="adv_opts"> 239 <xml name="adv_opts">
242 <!-- Other options --> 240 <!-- Other options -->
243 <param name="nonull2" type="boolean" truevalue="--nonull2" label="Turn off biased composition score corrections" help="(--nonull2)" falsevalue=""/> 241 <param argument="--nonull2" type="boolean" truevalue="--nonull2" falsevalue="" label="Turn off biased composition score corrections" />
244 <param name="Z" type="integer" label="# of comparisons done for E-value calculation" help="(-Z)" optional="True"/> 242 <param argument="-Z" type="integer" optional="true" label="# of comparisons done for E-value calculation" />
245 <param name="domZ" type="integer" label="# of significant sequences, for domain E-value calculation" help="(--domZ)" optional="True"/> 243 <param argument="--domZ" type="integer" optional="true" label="# of significant sequences, for domain E-value calculation" />
246 </xml> 244 </xml>
247 <token name="@FORMAT_SELECTOR@"> 245 <token name="@FORMAT_SELECTOR@">
248 $input_format_select 246 $input_format_select
249 </token> 247 </token>
250 <xml name="format_selector"> 248 <xml name="format_selector">
262 </xml> 260 </xml>
263 <token name="@ARSWS@"> 261 <token name="@ARSWS@">
264 $arsws.arsws_select 262 $arsws.arsws_select
265 263
266 #if $arsws.arsws_select == "--wblosum": 264 #if $arsws.arsws_select == "--wblosum":
267 --wid $arsws.wid 265 --wid $arsws.wid
268 #end if 266 #end if
269 </token> 267 </token>
270 <xml name="arsws"> 268 <xml name="arsws">
271 <!-- Alternative relative sequence weighting strategies --> 269 <!-- Alternative relative sequence weighting strategies -->
272 <conditional name="arsws"> 270 <conditional name="arsws">
280 <when value="--wpb"> 278 <when value="--wpb">
281 </when> 279 </when>
282 <when value="--wgsc"> 280 <when value="--wgsc">
283 </when> 281 </when>
284 <when value="--wblosum"> 282 <when value="--wblosum">
285 <param name="wid" label="Set identity cutoff" value="0.62" type="float" help="(--wid)"/> 283 <param argument="--wid" type="float" value="0.62" label="Set identity cutoff" />
286 </when> 284 </when>
287 <when value="--wnone"> 285 <when value="--wnone">
288 </when> 286 </when>
289 <when value="--wgiven"> 287 <when value="--wgiven">
290 </when> 288 </when>
313 <option value="enone">No effective seq # weighting: just use nseq (--enone)</option> 311 <option value="enone">No effective seq # weighting: just use nseq (--enone)</option>
314 </param> 312 </param>
315 <when value=""> 313 <when value="">
316 </when> 314 </when>
317 <when value="eent"> 315 <when value="eent">
318 <param name="eset" type="float" value="0" label="set eff seq # for all models" help="(--eset)"/> 316 <param argument="--eset" type="float" value="0" label="set eff seq # for all models" />
319 <param name="ere" type="float" value="0" label="set minimum rel entropy/position" help="(--ere)"/> 317 <param argument="--ere" type="float" value="0" label="set minimum rel entropy/position" />
320 <param name="esigma" type="float" value="45" label="set sigma param" help="(--esigma)"/> 318 <param argument="--esigma" type="float" value="45" label="set sigma param" />
321 </when> 319 </when>
322 <when value="eclust"> 320 <when value="eclust">
323 <param name="eset" type="float" value="0" label="set eff seq # for all models" help="(--eset)"/> 321 <param argument="--eset" type="float" value="0" label="set eff seq # for all models" />
324 <param name="eid" type="float" value="0.62" label="set fractional identity cutoff" min="0" max="1" help="(--eid)"/> 322 <param argument="--eid" type="float" min="0" max="1" value="0.62" label="set fractional identity cutoff" />
325 </when> 323 </when>
326 <when value="enone"> 324 <when value="enone">
327 </when> 325 </when>
328 </conditional> 326 </conditional>
329 </xml> 327 </xml>
331 $cut_ga 329 $cut_ga
332 $cut_nc 330 $cut_nc
333 $cut_tc 331 $cut_tc
334 </token> 332 </token>
335 <xml name="cut"> 333 <xml name="cut">
336 <param name="cut_ga" type="boolean" truevalue="--cut_ga" label="use profile's GA gathering cutoffs to set all thresholding" help="(--cut_ga)" falsevalue=""/> 334 <param argument="--cut_ga" type="boolean" truevalue="--cut_ga" falsevalue="" label="use profile's GA gathering cutoffs to set all thresholding" />
337 <param name="cut_nc" type="boolean" truevalue="--cut_nc" label="use profile's NC gathering cutoffs to set all thresholding" help="(--cut_nc)" falsevalue=""/> 335 <param argument="--cut_nc" type="boolean" truevalue="--cut_nc" falsevalue="" label="use profile's NC gathering cutoffs to set all thresholding" />
338 <param name="cut_tc" type="boolean" truevalue="--cut_tc" label="use profile's TC gathering cutoffs to set all thresholding" help="(--cut_tc)" falsevalue=""/> 336 <param argument="--cut_tc" type="boolean" truevalue="--cut_tc" falsevalue="" label="use profile's TC gathering cutoffs to set all thresholding" />
339 </xml> 337 </xml>
340 <token name="@MCSS@"> 338 <token name="@MCSS@">
341 --$mcs.model_construction_strategy_select 339 --$mcs.model_construction_strategy_select
342 340
343 #if $mcs.model_construction_strategy_select == "fast": 341 #if $mcs.model_construction_strategy_select == "fast":
344 --symfrac $mcs.symfrac 342 --symfrac $mcs.symfrac
345 #end if 343 #end if
346 344 #if str($fragthresh)
345 --fragthresh $fragthresh
346 #end if
347 </token> 347 </token>
348 <xml name="mcss"> 348 <xml name="mcss">
349 <!-- Alternative model construction strategies --> 349 <!-- Alternative model construction strategies -->
350 <conditional name="mcs"> 350 <conditional name="mcs">
351 <param name="model_construction_strategy_select" type="select" label="Model Construction Strategy"> 351 <param name="model_construction_strategy_select" type="select" label="Model Construction Strategy">
352 <option value="fast" selected="true">Assign columns with &gt;= symfrac residues as consensus (--fast)</option> 352 <option value="fast" selected="true">Assign columns with &gt;= symfrac residues as consensus (--fast)</option>
353 <option value="hand">Manual construction (requires reference annotation) (--hand)</option> 353 <option value="hand">Manual construction (requires reference annotation) (--hand)</option>
354 </param> 354 </param>
355 <when value="fast"> 355 <when value="fast">
356 <param name="symfrac" value="0.5" type="float" label="Sets sym fraction controlling --fast construction"/> 356 <param argument="--symfrac" value="0.5" type="float" label="Sets sym fraction controlling --fast construction"/>
357 </when> 357 </when>
358 <when value="hand"></when> 358 <when value="hand"></when>
359 </conditional> 359 </conditional>
360 <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" /> 360 <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" />
361
362 </xml> 361 </xml>
363 <token name="@PRIOR@"> 362 <token name="@PRIOR@">
364 $aps_select 363 $aps_select
365 </token> 364 </token>
366 <xml name="prior"> 365 <xml name="prior">
374 <citations> 373 <citations>
375 <citation type="doi">10.1093/nar/gkr367</citation> 374 <citation type="doi">10.1093/nar/gkr367</citation>
376 </citations> 375 </citations>
377 </xml> 376 </xml>
378 <token name="@LENGTHS@"> 377 <token name="@LENGTHS@">
379 #if $w_beta: 378 #if str($w_beta):
380 --w_beta $w_beta 379 --w_beta $w_beta
381 #end if 380 #end if
382 381
383 #if $w_length: 382 #if str($w_length):
384 --w_length $w_length 383 --w_length $w_length
385 #end if 384 #end if
386
387 </token> 385 </token>
388 <xml name="lengths"> 386 <xml name="lengths">
389 <param name="w_beta" label="Tail mass at which window length is determined" 387 <param argument="--w_beta" type="float" optional="true" label="Tail mass at which window length is determined" />
390 help="(--w_beta)" optional="True" type="float"/> 388 <param argument="--w_length" type="integer" optional="true" label="Window Length" />
391 <param name="w_length" label="Window Length" 389 </xml>
392 help="(--w_length)" optional="True" type="integer" /> 390 <token name="@INPUTHMMCHOICE@"><![CDATA[
393 </xml>
394 <token name="@INPUTHMMCHOICE@">
395 #if $input_hmm_conditional.input_hmm_source == "history": 391 #if $input_hmm_conditional.input_hmm_source == "history":
396 '$input_hmm_conditional.hmmfile' 392 #set $input_hmm_filename = "localref.hmm"
393 ln -s '${input_hmm_conditional.hmmfile}' '${input_hmm_filename}' &&
394 ## "Press" database
395 hmmpress '${input_hmm_filename}' &&
397 #else: 396 #else:
398 '$input_hmm_conditional.index.fields.db_path' 397 #set $input_hmm_filename = str($input_hmm_conditional.index.fields.db_path)
399 #end if 398 #end if
400 </token> 399 ]]></token>
401 <xml name="input_hmm_choice"> 400 <xml name="input_hmm_choice">
402 <conditional name="input_hmm_conditional"> 401 <conditional name="input_hmm_conditional">
403 <param name="input_hmm_source" type="select" label="Use a built-in HMM model database or own from your history" > 402 <param name="input_hmm_source" type="select" label="Use a built-in HMM model database or own from your history" >
404 <option value="indexed" selected="True">Use a built-in HMM model database</option> 403 <option value="indexed" selected="true">Use a built-in HMM model database</option>
405 <option value="history">Use a HMM database from history</option> 404 <option value="history">Use a HMM database from history</option>
406 </param> 405 </param>
407 <when value="indexed"> 406 <when value="indexed">
408 <param name="index" type="select" label="Select a HMM model database" help="If your database of interest is not listed, contact the Galaxy administrator"> 407 <param name="index" type="select" label="Select a HMM model database" help="If your database of interest is not listed, contact the Galaxy administrator">
409 <options from_data_table="hmm_database"> 408 <options from_data_table="hmm_database">
411 <validator type="no_options" message="No indexes are available for the selected input dataset"/> 410 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
412 </options> 411 </options>
413 </param> 412 </param>
414 </when> 413 </when>
415 <when value="history"> 414 <when value="history">
416 <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/> 415 <param name="hmmfile" type="data" format="hmm2,hmm3" label="HMM model" />
417 </when> <!-- history --> 416 </when> <!-- history -->
418 </conditional> <!-- input_hmm_conditional --> 417 </conditional> <!-- input_hmm_conditional -->
419 </xml> 418 </xml>
420 <xml name="input_hmm"> 419 <xml name="input_hmm">
421 <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/> 420 <param name="hmmfile" type="data" format="hmm2,hmm3" label="HMM model" />
422 </xml> 421 </xml>
423 <xml name="input_msa"> 422 <xml name="input_msa">
424 <param name="msafile" type="data" label="Multiple Sequence Alignment" format="stockholm,clustal,fasta" 423 <param name="msafile" type="data" label="Multiple Sequence Alignment" format="stockholm,clustal,fasta"
425 help="in Stockholm, Clustal, or Fasta format. While this tool accepts fasta, please ensure that the sequences are not unaligned"/> 424 help="in Stockholm, Clustal, or Fasta format. While this tool accepts fasta, please ensure that the sequences are not unaligned"/>
426 </xml> 425 </xml>