Mercurial > repos > iuc > hyphy_annotate

comparison macros.xml @ 2:2219b0ceb19e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 17:48:06 +0000
parents be1650bef38c
children f5de1dc64fd6
comparison
equal deleted inserted replaced
1:6f7070ccde66 2:2219b0ceb19e
91 <option value="Blepharisma-Nuclear">Blepharisma Nuclear 91 <option value="Blepharisma-Nuclear">Blepharisma Nuclear
92 code</option> 92 code</option>
93 </param> 93 </param>
94 </xml> 94 </xml>
95 95
96 <xml name="srv">
97 <conditional name="advanced" label="Advanced options">
98 <param name="srv_options" type="select" label="Set advanced parameters" help="If these parameters are not set, RELAX will calculate appropriate values at runtime">
99 <option value="defaults">Calculate</option>
100 <option value="specify">Specify values</option>
101 </param>
102 <when value="defaults" />
103 <when value="specify">
104 <param argument="--grid-size" type="integer" value="250" label="Points in the initial distributional guess for likelihood fitting" />
105 <param argument="--starting-points" type="integer" value="1" label="Initial random guesses to seed rate values optimization" />
106 <param argument="--syn-rates" type="integer" min="1" max="10" value="3" label="Alpha rate classes to include in the model" />
107 <param argument="--rates" type="integer" min="2" max="10" value="3" label="Omega rate classes to include in the model" />
108 <param argument="--srv" type="boolean" truevalue="Yes" falsevalue="No" label="Include synonymous rate variation" />
109 <param name="save_alternative_model" type="boolean" label="Save alternative model fit" />
110 </when>
111 </conditional>
112 </xml>
113
96 <xml name="branches"> 114 <xml name="branches">
97 <param name="branches" type="select" label="Set of branches to test"> 115 <conditional name="branch_cond">
98 <option value="All">All branches</option> 116 <param name="branch_sel" type="select" label="Set of branches to test">
99 <option value="Internal">Internal branches</option> 117 <option value="All">All branches</option>
100 <option value="Leaves">Leaf branches</option> 118 <option value="Internal">Internal branches</option>
101 <option value="'Unlabeled-branches'">Unlabeled branches</option> 119 <option value="Leaves">Leaf branches</option>
102 </param> 120 <option value="'Unlabeled-branches'">Unlabeled branches</option>
121 <option value="specify">Enter a branch label</option>
122 </param>
123 <when value="specify">
124 <param name="branch_label" type="text" value="Test" optional="false" label="Branch label">
125 <sanitizer invalid_char="">
126 <valid initial="default" />
127 </sanitizer>
128 </param>
129 </when>
130 <when value="All" />
131 <when value="Internal" />
132 <when value="Leaves" />
133 <when value="'Unlabeled-branches'" />
134 </conditional>
103 </xml> 135 </xml>
104 <xml name="citations"> 136 <xml name="citations">
105 <citations> 137 <citations>
106 <citation type="doi">10.1093/molbev/msz197</citation> 138 <citation type="doi">10.1093/molbev/msz197</citation>
107 <yield/> 139 <yield/>
112 <requirements> 144 <requirements>
113 <requirement type="package" version="@VERSION@">hyphy</requirement> 145 <requirement type="package" version="@VERSION@">hyphy</requirement>
114 <yield/> 146 <yield/>
115 </requirements> 147 </requirements>
116 </xml> 148 </xml>
149 <xml name="alternative_model_output">
150 <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json">
151 <filter>advanced['save_alternative_model']</filter>
152 </data>
153 </xml>
154 <token name="@INPUT_TREE@"><![CDATA[
155 #if $input_nhx:
156 --tree input.nhx
157 #end if
158 ]]>
159 </token>
160 <token name="@branch_options@"><![CDATA[
161 #if $branch_cond.branch_sel == 'specify':
162 --branches '$branch_cond.branch_label'
163 #else:
164 --branches $branch_cond.branch_sel
165 #end if
166 ]]>
167 </token>
168 <token name="@advanced_options@"><![CDATA[
169 #if $advanced.srv_options == 'specify':
170 --grid-size $advanced.grid_size
171 --starting-points $advanced.starting_points
172 --syn-rates $advanced.syn_rates
173 --rates $advanced.rates
174 --srv $advanced.srv
175 #if $advanced.save_alternative_model:
176 --save-fit alternative_model.json
177 #end if
178 #end if
179 ]]></token>
117 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> 180 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
118 <token name="@CATCH_ERROR@"><![CDATA[ 181 <token name="@ERRORS@"><![CDATA[
119 EC=\$? ; 182 ; EC=\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; exit \$EC
120 if [ \$EC -ne 0 ] ; then
121 if [ -f errors.log.mpinode0 ] ; then
122 cat errors.log.mpinode0 >&2 ;
123 else
124 cat errors.log >&2 ;
125 fi ;
126 fi ;
127 exit \$EC
128 ]]></token> 183 ]]></token>
129 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[ 184 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[
130 export HYPHY=`which hyphy` && 185 export HYPHY=`which hyphy` &&
131 export HYPHY_PATH=`dirname \$HYPHY` && 186 export HYPHY_PATH=`dirname \$HYPHY` &&
132 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &&]]></token> 187 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &&]]></token>
133 <token name="@HYPHY_INVOCATION@"><![CDATA[ 188 <token name="@HYPHY_INVOCATION@"><![CDATA[
134 @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB 189 @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB
135 ]]></token> 190 ]]></token>
136 <token name="@SYMLINK_FILES@"><![CDATA[ 191 <token name="@SYMLINK_FILES@"><![CDATA[
137 ln -s '$input_file' input.$input_file.extension && 192 #if $input_nhx is not None:
138 ln -s '$@operation@_output' input.${input_file.extension}.@OPERATION@.json &&
139 #set $input_file = 'input.%s' % $input_file.extension
140 #if $input_nhx:
141 ln -s '$input_nhx' input.nhx && 193 ln -s '$input_nhx' input.nhx &&
142 #end if 194 #end if
195 ln -s '$input_file' input.$input_file.extension &&
196 #set $input_file = 'input.%s' % $input_file.extension
143 ]]></token> 197 ]]></token>
144 </macros> 198 </macros>