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comparison macros.xml @ 5:5113c71c7031 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
author iuc
date Tue, 16 Jun 2020 05:32:33 -0400
parents 793967b6ae8a
children d9ce554da9b4
comparison
equal deleted inserted replaced
4:793967b6ae8a 5:5113c71c7031
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> 8 </xml>
9 <token name="@TOOL_VERSION@">3.2</token> 9 <token name="@TOOL_VERSION@">3.3</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"/>
112 <param argument="--EvN" type="integer" min="1" value="200" 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" />
113 <param argument="--EfL" type="integer" min="1" value="100" 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" />
114 <param argument="--EfN" type="integer" min="1" value="200" 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" />
115 <param argument="--Eft" type="float" min="0" max="1" value="0.04" 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" />
116 </xml> 116 </xml>
117 <token name="@OFORMAT_WITH_OPTS_NOPFAM@"> 117 <token name="@OFORMAT_WITH_OPTS@">
118 #if 'tblout' in str($oformat): 118 #if $oformat:
119 --tblout '$tblout' 119 #for o in str($oformat).split(','):
120 #end if 120 --$o '$getVar($o, 'MISSING_OUTPUT'+$o)'
121 121 #end for
122 #if 'domtblout' in str($oformat): 122 #end if
123 --domtblout '$domtblout'
124 #end if
125
126 $acc $noali $notextw 123 $acc $noali $notextw
127 </token> 124 </token>
128 <xml name="oformat_with_opts_nopfam"> 125 <xml name="oformat_with_opts">
129 <!-- Options directing output --> 126 <!-- Options directing output -->
130 <param name="oformat" multiple="true" display="checkboxes" label="Output Formats" type="select"> 127 <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats">
131 <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option> 128 <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
132 <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option> 129 <yield/>
133 </param> 130 </param>
134 <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" /> 131 <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" />
135 <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" /> 132 <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" />
136 <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" /> 133 <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" />
137 </xml> 134 </xml>
138 <token name="@OFORMAT_WITH_OPTS@"> 135
139 #if 'tblout' in str($oformat): 136 <xml name="oformat_with_opts_dom">
140 --tblout '$tblout' 137 <expand macro="oformat_with_opts">
141 #end if 138 <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
142 139 <yield/>
143 #if 'domtblout' in str($oformat): 140 </expand>
144 --domtblout '$domtblout' 141 </xml>
145 #end if 142
146 143 <xml name="oformat_with_opts_dom_pfam">
147 #if 'pfamtblout' in str($oformat): 144 <expand macro="oformat_with_opts_dom">
148 --pfamtblout '$pfamtblout' 145 <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option>
149 #end if 146 </expand>
150 147 </xml>
151 $acc $noali $notextw 148
152 </token> 149 <xml name="oformat_with_opts_dfam_alisc">
153 <xml name="oformat_with_opts">
154 <!-- Options directing output --> 150 <!-- Options directing output -->
155 <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats"> 151 <expand macro="oformat_with_opts">
156 <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option> 152 <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option>
157 <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option> 153 <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option>
158 <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option> 154 </expand>
159 </param> 155 </xml>
160 <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" /> 156
161 <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" /> 157 <xml name="output" token_tool="">
162 <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" /> 158 <data name="output" format="txt" label="@TOOL@ on ${on_string}"/>
163 </xml> 159 <data name="tblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence hits from HMM matches">
160 <filter>oformat and 'tblout' in oformat</filter>
161 </data>
162 <yield/>
163 </xml>
164 <xml name="output_dom" token_tool="">
165 <expand macro="output" tool="@TOOL@">
166 <data name="domtblout" format="txt" label="@TOOL@ on ${on_string}: per-domain hits from HMM matches">
167 <filter>oformat and 'domtblout' in oformat</filter>
168 </data>
169 </expand>
170 <yield/>
171 </xml>
172 <xml name="output_dom_pfam" token_tool="">
173 <expand macro="output_dom" tool="@TOOL@">
174 <data name="pfamtblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence/per-domain hits from HMM matches">
175 <filter>oformat and 'pfamtblout' in oformat</filter>
176 </data>
177 </expand>
178 </xml>
179 <xml name="output_dfam_alisc" token_tool="" token_ofvar="seqfile" token_invar="seqdb">
180 <expand macro="output" tool="@TOOL@">
181 <data name="dfamtblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence/per-domain hits from HMM matches">
182 <filter>oformat and 'dfamtblout' in oformat</filter>
183 </data>
184 <data name="aliscoresout" format="txt" label="@TOOL@ on ${on_string}: scores for positional matches">
185 <filter>oformat and 'aliscoresout' in oformat</filter>
186 </data>
187 </expand>
188 </xml>
189
190 <xml name="assert_out" token_tool="">
191 <assert_contents>
192 <has_line_matching expression="# @TOOL@.*"/>
193 <has_line_matching expression="\[ok\]"/>
194 </assert_contents>
195 </xml>
196
197 <xml name="assert_tblout" token_tool="">
198 <assert_contents>
199 <has_line_matching expression="# Program: @TOOL@"/>
200 <has_line_matching expression="# \[ok\]"/>
201 </assert_contents>
202 </xml>
203
164 <xml name="oformat_test"> 204 <xml name="oformat_test">
165 <param name="notextw" value="true" /> 205 <param name="notextw" value="true" />
166 </xml>
167 <!-- TODO: tblout will match 'pfamtblout,dfamtblout' -->
168 <token name="@OFORMAT_WITH_OPTS_N@">
169 #if 'tblout' in str($oformat):
170 --tblout '$tblout'
171 #end if
172
173 #if 'dfamtblout' in str($oformat):
174 --dfamtblout '$dfamtblout'
175 #end if
176
177 #if 'aliscoresout' in str($oformat):
178 --aliscoresout '$aliscoresout'
179 #end if
180
181 $acc $noali $notextw
182 </token>
183 <xml name="oformat_with_opts_n">
184 <!-- Options directing output -->
185 <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats">
186 <option value="tblout" selected="true">Table of hits (--tblout)</option>
187 <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option>
188 <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option>
189 </param>
190 <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" />
191 <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" />
192 <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" />
193 </xml> 206 </xml>
194 <token name="@HSSI@"> 207 <token name="@HSSI@">
195 #if $hssi.hssi_select == "singlemx": 208 #if $hssi.hssi_select == "singlemx":
196 --popen $hssi.popen 209 --popen $hssi.popen
197 --pextend $hssi.pextend 210 --pextend $hssi.pextend
1075 # HMMER 3.1 (February 2013); http://hmmer.org/ 1088 # HMMER 3.1 (February 2013); http://hmmer.org/
1076 # Copyright (C) 2011 Howard Hughes Medical Institute. 1089 # Copyright (C) 2011 Howard Hughes Medical Institute.
1077 # Freely distributed under the GNU General Public License (GPLv3). 1090 # Freely distributed under the GNU General Public License (GPLv3).
1078 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1091 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
1079 1092
1080 The wrappers were written by Eric Rasche and is licensed under Apache2_. The 1093 The wrappers were written by the IUC and are licensed under Apache2_. The
1081 documentation is copied from the HMMER3 documentation. 1094 documentation is copied from the HMMER3 documentation.
1082 1095
1083 .. _Apache2: http://www.apache.org/licenses/LICENSE-2.0 1096 .. _Apache2: http://www.apache.org/licenses/LICENSE-2.0
1084 .. _HMMER3: http://hmmer.org/ 1097 .. _HMMER3: http://hmmer.org/
1085 1098