Mercurial > repos > iuc > hyphy_absrel

comparison hyphy_absrel.xml @ 16:4cc4dbca2f02 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
author iuc
date Fri, 18 Sep 2020 21:10:47 +0000
parents cce7b18495e4
children 0b58ef9e84b2
comparison
equal deleted inserted replaced
15:81e66674859e 16:4cc4dbca2f02
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0"> 2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy1">
3 <description>adaptive Branch Site Random Effects Likelihood</description> 3 <description>adaptive Branch Site Random Effects Likelihood</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
12 --alignment ./absrel_input.fa 12 --alignment ./absrel_input.fa
13 --tree ./absrel_input.nhx 13 --tree ./absrel_input.nhx
14 --code '$gencodeid' 14 --code '$gencodeid'
15 --branches '$branches' 15 --branches '$branches'
16 --output '$absrel_output' 16 --output '$absrel_output'
17 --multiple-hits $multiple_hits
17 #if $log: 18 #if $log:
18 > '$absrel_log' 19 > '$absrel_log'
19 #end if 20 #end if
20 ; 21 ;
21 @CATCH_MPIERR@ 22 @CATCH_MPIERR@
22 ]]></command> 23 ]]></command>
23 <inputs> 24 <inputs>
24 <expand macro="inputs"/> 25 <expand macro="inputs"/>
25 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/> 26 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
26 <expand macro="gencode"/> 27 <expand macro="gencode"/>
28 <param name="multiple_hits" type="select" argument="--multiple-hits" label="Include support for multiple nucleotide substitutions">
29 <option value="None">Use standard models which permit only single nucleotide changes to occur instantly</option>
30 <option value="Double">Include branch-specific rates for double nucleotide substitutions</option>
31 <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option>
32 </param>
27 <expand macro="branches"/> 33 <expand macro="branches"/>
28 </inputs> 34 </inputs>
29 <outputs> 35 <outputs>
30 <data name="absrel_log" format="txt"> 36 <data name="absrel_log" format="txt">
31 <filter>log</filter> 37 <filter>log</filter>
34 </outputs> 40 </outputs>
35 <tests> 41 <tests>
36 <test> 42 <test>
37 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> 43 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
38 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> 44 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
45 <param name="multiple_hits" value="None" />
46 <param name="log" value="false"/>
47 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
48 </test>
49 <test>
50 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
51 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
52 <param name="multiple_hits" value="Double" />
39 <param name="log" value="false"/> 53 <param name="log" value="false"/>
40 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/> 54 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
41 </test> 55 </test>
42 </tests> 56 </tests>
43 <help><![CDATA[ 57 <help><![CDATA[