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comparison macros.xml @ 8:923db0592cd0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 061757dd7b3bfe66b7738fd54bd6c5e135d9afe8
author iuc
date Mon, 06 Nov 2023 20:26:19 +0000
parents dc8860ba75d1
children 4b996c837ec8
comparison
equal deleted inserted replaced
7:dc8860ba75d1 8:923db0592cd0
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="@TOOL_VERSION@">hmmer</requirement> 5 <requirement type="package" version="@TOOL_VERSION@">hmmer</requirement>
6 <yield/> 6 <yield/>
7 </requirements> 7 </requirements>
8 </xml>
9 <xml name="bio_tools">
10 <xrefs>
11 <xref type="bio.tools">hmmer3</xref>
12 </xrefs>
8 </xml> 13 </xml>
9 <token name="@TOOL_VERSION@">3.3.2</token> 14 <token name="@TOOL_VERSION@">3.3.2</token>
10 <xml name="stdio"> 15 <xml name="stdio">
11 <stdio> 16 <stdio>
12 <!-- Anything other than zero is an error --> 17 <!-- Anything other than zero is an error -->
15 <!-- In case the return code has not been set propery check stderr too --> 20 <!-- In case the return code has not been set propery check stderr too -->
16 <regex match="Error:"/> 21 <regex match="Error:"/>
17 <regex match="Exception:"/> 22 <regex match="Exception:"/>
18 </stdio> 23 </stdio>
19 </xml> 24 </xml>
25
26 <!-- command line for thresholds_* -->
20 <token name="@THRESHOLDS@"> 27 <token name="@THRESHOLDS@">
21 -E $E 28 #if $repopt.repopt_sel == "evalue"
22 --domE $domE 29 -E $repopt.E
23 30 #if str($repopt.incE) != ""
24 #if str($T): 31 --incE $repopt.incE
25 -T $T 32 #end if
26 #end if 33 #elif $repopt.repopt_sel == "score"
27 34 -T $repopt.T
28 #if str($domT): 35 #if str($repopt.incT) != ""
29 --domT $domT 36 --incT $repopt.incT
30 #end if 37 #end if
31 38 #else
32 #if str($incE): 39 $repopt.repopt_sel
33 --incE $incE 40 #end if
34 #end if 41 </token>
35 42 <!-- additional command line thresholds*dom* -->
36 #if str($incdomE): 43 <token name="@THRESHOLDS_DOM@">
37 --incdomE $incdomE 44 #if $repopt.repopt_sel == "evalue"
38 #end if 45 --domE $repopt.domE
39 46 #if str($repopt.incdomE) != ""
40 #if str($incT): 47 --incdomE $repopt.incdomE
41 --incT $incT 48 #end if
42 #end if 49 #elif $repopt.repopt_sel == "score"
43 50 --domT $repopt.domT
44 #if str($incdomT): 51 #if str($repopt.incdomT) != ""
45 --incdomT $incdomT 52 --incdomT $repopt.incdomT
46 #end if 53 #end if
47 </token> 54 #end if
55 </token>
56
48 <xml name="thresholds_xml"> 57 <xml name="thresholds_xml">
49 <!-- Options controlling reporting thresholds -->
50 <param argument="-E" type="float" min="0" value="10.0" label="report sequences &lt;= this E-Value threshold in output" />
51 <param argument="--domE" type="float" min="0" value="10.0" label="report domains &lt;= this E-Value threshold in output" />
52 <param argument="-T" type="float" optional="true" label="report sequences &gt;= this score threshold in output" />
53 <param argument="--domT" type="float" optional="true" label="report domains &gt;= this score threshold in output" />
54 <!-- Options controlling inclusion (significance) thresholds --> 58 <!-- Options controlling inclusion (significance) thresholds -->
55 <param argument="--incE" type="float" optional="true" label="consider sequences &lt;= this E-Value threshold as significant" /> 59 <conditional name="repopt">
60 <param name="repopt_sel" type="select" label="Threshold option">
61 <option value="evalue" selected="true">E-value (reporting threshold)</option>
62 <option value="score">Score (reporting threshold)</option>
63 <yield name="additional_options"/>
64 </param>
65 <when value="evalue">
66 <param argument="-E" type="float" min="0" value="10" label="E-value threshold" help="Report sequences &lt;= this E-Value threshold in output. Default: 10.0" />
67 <param argument="--incE" type="float" optional="true" label="consider sequences &lt;= this E-Value threshold as significant" />
68 <yield name="edom_params"/>
69 </when>
70 <when value="score">
71 <param argument="-T" type="float" value="" label="Score Threshold" help="Report sequences &gt;= this score threshold in output. This option is incompatible with -E, --cut_ga,--cut_nc" />
72 <param argument="--incT" type="float" optional="true" label="consider sequences &gt;= this score threshold as significant" />
73 <yield name="tdom_params"/>
74 </when>
75 <yield name="additional_whens"/>
76 </conditional>
77 </xml>
78
79 <xml name="thresholds_dom_xml">
80 <expand macro="thresholds_xml">
81 <token name="edom_params">
82 <expand macro="dome_thresholds"/>
83 </token>
84 <token name="tdom_params">
85 <expand macro="domt_thresholds"/>
86 </token>
87 </expand>
88 </xml>
89
90 <xml name="thresholds_cut_xml">
91 <expand macro="thresholds_xml">
92 <token name="additional_options">
93 <expand macro="model_specific_options"/>
94 </token>
95 <token name="additional_whens">
96 <expand macro="model_specific_whens"/>
97 </token>
98 </expand>
99 </xml>
100
101 <xml name="thresholds_cut_dom_xml">
102 <expand macro="thresholds_xml">
103 <token name="edom_params">
104 <expand macro="dome_thresholds"/>
105 </token>
106 <token name="tdom_params">
107 <expand macro="domt_thresholds"/>
108 </token>
109 <token name="additional_options">
110 <expand macro="model_specific_options"/>
111 </token>
112 <token name="additional_whens">
113 <expand macro="model_specific_whens"/>
114 </token>
115 </expand>
116 </xml>
117
118 <xml name="model_specific_options">
119 <option value="--cut_ga">Use profile's GA gathering cutoffs (model specific threshold)</option>
120 <option value="--cut_nc">Use profile's NC gathering cutoffs (model specific threshold)</option>
121 <option value="--cut_tc">Use profile's TC gathering cutoffs (model specific threshold)</option>
122 </xml>
123
124 <xml name="model_specific_whens">
125 <when value="--cut_ga"/>
126 <when value="--cut_nc"/>
127 <when value="--cut_tc"/>
128 </xml>
129
130 <xml name="dome_thresholds">
131 <param argument="--domE" type="float" min="0" value="10" label="Domains E-value threshold" help="Report domains &lt;= this E-Value threshold in output. Default: 10.0. This option is incompatible with --domT, --cut_ga" />
56 <param argument="--incdomE" type="float" optional="true" label="consider domains &lt;= this E-Value threshold as significant" /> 132 <param argument="--incdomE" type="float" optional="true" label="consider domains &lt;= this E-Value threshold as significant" />
57 <param argument="--incT" type="float" optional="true" label="consider sequences &gt;= this score threshold as significant" /> 133 </xml>
134
135 <xml name="domt_thresholds">
136 <param argument="--domT" type="float" value="" label="Domains Score Threshold" help="Report domains &gt;= this score threshold in output. This option is incompatible with --domE, --cut_ga" />
58 <param argument="--incdomT" type="float" optional="true" label="consider domains &gt;= this score threshold as significant" /> 137 <param argument="--incdomT" type="float" optional="true" label="consider domains &gt;= this score threshold as significant" />
59 </xml> 138 </xml>
60 <token name="@THRESHOLDS_NODOM@"> 139
61 -E $E
62
63 #if str($T):
64 -T $T
65 #end if
66
67 #if str($incE):
68 --incE $incE
69 #end if
70
71 #if str($incT):
72 --incT $incT
73 #end if
74 </token>
75 <xml name="thresholds_nodom"> 140 <xml name="thresholds_nodom">
76 <!-- Options controlling reporting thresholds --> 141 <!-- Options controlling reporting thresholds -->
77 <param argument="-E" type="float" min="0" value="10.0" label="report sequences &lt;= this E-Value threshold in output" /> 142 <param argument="-E" type="float" min="0" optional="true" label="E-Value Threshold" help="Report sequences &lt;= this E-Value threshold in output. Default: 10.0. This option is incompatible with option -T,--cut_ga, --cut_nc" />
78 <param argument="-T" type="float" optional="true" label="report sequences &gt;= this score threshold in output" /> 143 <param argument="-T" type="float" optional="true" label="Score Threshold" help="Report sequences &gt;= this score threshold in output. This option is incompatible with -E, --cut_ga,--cut_nc" />
79 <!-- Options controlling inclusion (significance) thresholds --> 144 <!-- Options controlling inclusion (significance) thresholds -->
80 <param argument="--incE" type="float" optional="true" label="consider sequences &lt;= this E-Value threshold as significant" /> 145 <param argument="--incE" type="float" optional="true" label="consider sequences &lt;= this E-Value threshold as significant" />
81 <param argument="--incT" type="float" optional="true" label="consider sequences &gt;= this score threshold as significant" /> 146 <param argument="--incT" type="float" optional="true" label="consider sequences &gt;= this score threshold as significant" />
82 </xml> 147 </xml>
148 <xml name="cut">
149 <param argument="--cut_ga" type="boolean" truevalue="--cut_ga" falsevalue="" label="use profile's GA gathering cutoffs to set all thresholding" help="This option is incompatible with options -E,-T,--domE,--domT" />
150 <param argument="--cut_nc" type="boolean" truevalue="--cut_nc" falsevalue="" label="use profile's NC gathering cutoffs to set all thresholding" help="This option is incompatible with options -E,-T,--domE,--domT" />
151 <param argument="--cut_tc" type="boolean" truevalue="--cut_tc" falsevalue="" label="use profile's TC gathering cutoffs to set all thresholding" />
152 </xml>
153
83 <token name="@ACCEL_HEUR@"> 154 <token name="@ACCEL_HEUR@">
84 $max 155 $max
85 --F1 $F1 156 --F1 $F1
86 --F2 $F2 157 --F2 $F2
87 --F3 $F3 158 --F3 $F3
113 <param argument="--EfL" type="integer" min="1" value="100" label="Length of sequences for Forward exp tail tau fit" /> 184 <param argument="--EfL" type="integer" min="1" value="100" label="Length 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" /> 185 <param argument="--EfN" type="integer" min="1" value="200" label="Number of sequences for Forward exp 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" /> 186 <param argument="--Eft" type="float" min="0" max="1" value="0.04" label="tail mass for Forward exponential tail tau fit" />
116 </xml> 187 </xml>
117 <token name="@OFORMAT_WITH_OPTS@"> 188 <token name="@OFORMAT_WITH_OPTS@">
118 #if $oformat: 189 #if $oformat:
119 #for o in str($oformat).split(','): 190 #for o in str($oformat).split(','):
120 --$o '$getVar($o, 'MISSING_OUTPUT'+$o)' 191 --$o '$getVar($o, 'MISSING_OUTPUT'+$o)'
121 #end for 192 #end for
122 #end if 193 #end if
123 $acc $noali $notextw 194 $acc $noali $notextw
142 213
143 <xml name="oformat_with_opts_dom_pfam"> 214 <xml name="oformat_with_opts_dom_pfam">
144 <expand macro="oformat_with_opts_dom"> 215 <expand macro="oformat_with_opts_dom">
145 <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option> 216 <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option>
146 </expand> 217 </expand>
147 </xml> 218 </xml>
148 219
149 <xml name="oformat_with_opts_dfam_alisc"> 220 <xml name="oformat_with_opts_dfam_alisc">
150 <!-- Options directing output --> 221 <!-- Options directing output -->
151 <expand macro="oformat_with_opts"> 222 <expand macro="oformat_with_opts">
152 <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option> 223 <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option>
190 <xml name="assert_out" token_tool=""> 261 <xml name="assert_out" token_tool="">
191 <assert_contents> 262 <assert_contents>
192 <has_line_matching expression="# @TOOL@.*"/> 263 <has_line_matching expression="# @TOOL@.*"/>
193 <has_line_matching expression="\[ok\]"/> 264 <has_line_matching expression="\[ok\]"/>
194 </assert_contents> 265 </assert_contents>
195 </xml> 266 </xml>
196 267
197 <xml name="assert_tblout" token_tool=""> 268 <xml name="assert_tblout" token_tool="">
198 <assert_contents> 269 <assert_contents>
199 <has_line_matching expression="# Program: @TOOL@"/> 270 <has_line_matching expression="# Program: @TOOL@"/>
200 <has_line_matching expression="# \[ok\]"/> 271 <has_line_matching expression="# \[ok\]"/>
201 </assert_contents> 272 </assert_contents>
202 </xml> 273 </xml>
203 274
204 <xml name="oformat_test"> 275 <xml name="oformat_test">
205 <param name="notextw" value="true" /> 276 <param name="notextw" value="true" />
206 </xml> 277 </xml>
207 <token name="@HSSI@"> 278 <token name="@HSSI@">
339 <param argument="--eid" type="float" min="0" max="1" value="0.62" label="set fractional identity cutoff" /> 410 <param argument="--eid" type="float" min="0" max="1" value="0.62" label="set fractional identity cutoff" />
340 </when> 411 </when>
341 <when value="enone"> 412 <when value="enone">
342 </when> 413 </when>
343 </conditional> 414 </conditional>
344 </xml>
345 <token name="@CUT@">
346 $cut_ga
347 $cut_nc
348 $cut_tc
349 </token>
350 <xml name="cut">
351 <param argument="--cut_ga" type="boolean" truevalue="--cut_ga" falsevalue="" label="use profile's GA gathering cutoffs to set all thresholding" />
352 <param argument="--cut_nc" type="boolean" truevalue="--cut_nc" falsevalue="" label="use profile's NC gathering cutoffs to set all thresholding" />
353 <param argument="--cut_tc" type="boolean" truevalue="--cut_tc" falsevalue="" label="use profile's TC gathering cutoffs to set all thresholding" />
354 </xml> 415 </xml>
355 <token name="@MCSS@"> 416 <token name="@MCSS@">
356 --$mcs.model_construction_strategy_select 417 --$mcs.model_construction_strategy_select
357 418
358 #if $mcs.model_construction_strategy_select == "fast": 419 #if $mcs.model_construction_strategy_select == "fast":