Mercurial > repos > iuc > hyphy_gard

comparison macros.xml @ 23:fc4012ea4c38 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author iuc
date Tue, 20 Apr 2021 10:11:30 +0000
parents b2955daefba5
children a453c5399072
comparison
equal deleted inserted replaced
22:b2955daefba5 23:fc4012ea4c38
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="inputs"> 3 <xml name="inputs">
4 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> 4 <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" />
5 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/> 5 <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>
6 </xml> 6 </xml>
7 <xml name="substitution"> 7 <xml name="substitution">
8 <param name="model" type="select" label="Substitution model"> 8 <param name="model" type="select" label="Substitution model">
9 <option value="GTR">GTR - General time reversible 9 <option value="GTR">GTR - General time reversible
10 model</option> 10 model</option>
105 <citations> 105 <citations>
106 <citation type="doi">10.1093/molbev/msz197</citation> 106 <citation type="doi">10.1093/molbev/msz197</citation>
107 <yield/> 107 <yield/>
108 </citations> 108 </citations>
109 </xml> 109 </xml>
110 <token name="@VERSION@">2.5.30</token> 110 <token name="@VERSION@">2.5.31</token>
111 <xml name="requirements"> 111 <xml name="requirements">
112 <requirements> 112 <requirements>
113 <requirement type="package" version="@VERSION@">hyphy</requirement> 113 <requirement type="package" version="@VERSION@">hyphy</requirement>
114 <yield/> 114 <yield/>
115 </requirements> 115 </requirements>
116 </xml> 116 </xml>
117 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> 117 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
118 <token name="@CATCH_MPIERR@"><![CDATA[ 118 <token name="@CATCH_ERROR@"><![CDATA[
119 EC=\$? ; 119 EC=\$? ;
120 if [ \$EC -ne 0 ] ; then 120 if [ \$EC -ne 0 ] ; then
121 cat errors.log.mpinode0 >&2 ; 121 if [ -f errors.log.mpinode0 ] ; then
122 cat errors.log.mpinode0 >&2 ;
123 else
124 cat errors.log >&2 ;
125 fi ;
122 fi ; 126 fi ;
123 exit \$EC 127 exit \$EC
124 ]]></token> 128 ]]></token>
125 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[ 129 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[
126 export HYPHY=`which hyphy` && 130 export HYPHY=`which hyphy` &&
127 export HYPHY_PATH=`dirname \$HYPHY` && 131 export HYPHY_PATH=`dirname \$HYPHY` &&
128 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &&]]></token> 132 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &&]]></token>
129 <token name="@HYPHY_INVOCATION@"><![CDATA[ 133 <token name="@HYPHY_INVOCATION@"><![CDATA[
130 @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB 134 @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB
131 ]]></token> 135 ]]></token>
136 <token name="@SYMLINK_FILES@"><![CDATA[
137 ln -s '$input_file' input.$input_file.extension &&
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 &&
142 #end if
143 ]]></token>
132 </macros> 144 </macros>