Mercurial > repos > iuc > hmmer_jackhmmer
comparison macros.xml @ 5:5113c71c7031 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
author | iuc |
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date | Tue, 16 Jun 2020 05:32:33 -0400 |
parents | 793967b6ae8a |
children | d9ce554da9b4 |
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4:793967b6ae8a | 5:5113c71c7031 |
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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 |