Mercurial > repos > iuc > hyphy_absrel

comparison hyphy_absrel.xml @ 3:ba0b2eda907d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
author iuc
date Fri, 14 Feb 2020 21:38:12 +0000
parents 68d3a06a4d9b
children 8c79739da199
comparison
equal deleted inserted replaced
2:68d3a06a4d9b 3:ba0b2eda907d
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"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$input_file' absrel_input.fa && 9 ln -s '$input_file' absrel_input.fa &&
10 ln -s '$input_nhx' absrel_input.nhx && 10 ln -s '$input_nhx' absrel_input.nhx &&
11 @HYPHY_INVOCATION@ absrel 11 @HYPHYMPI@ absrel
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 > '$absrel_log' 16 --output '$absrel_output'
17 #if $log:
18 > '$absrel_log'
19 #end if
17 ]]></command> 20 ]]></command>
18 <inputs> 21 <inputs>
19 <expand macro="inputs"/> 22 <expand macro="inputs"/>
20 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/> 23 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
21 <expand macro="gencode"/> 24 <expand macro="gencode"/>
23 </inputs> 26 </inputs>
24 <outputs> 27 <outputs>
25 <data name="absrel_log" format="txt"> 28 <data name="absrel_log" format="txt">
26 <filter>log</filter> 29 <filter>log</filter>
27 </data> 30 </data>
28 <data name="absrel_output" format="hyphy_results.json" from_work_dir="absrel_input.fa.ABSREL.json"/> 31 <data name="absrel_output" format="hyphy_results.json" />
29 </outputs> 32 </outputs>
30 <tests> 33 <tests>
31 <test> 34 <test>
32 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> 35 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
33 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> 36 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>