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comparison hyphy_relax.xml @ 25:a4c5dc437558 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 18:03:51 +0000
parents 801547975424
children 3415a580926d
comparison
equal deleted inserted replaced
24:098451b762fb 25:a4c5dc437558
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0" profile="19.09"> 2 <tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy1" profile="19.09">
3 <description>Detect relaxed selection in a codon-based 3 <description>Detect relaxed selection in a codon-based
4 phylogenetic framework</description> 4 phylogenetic framework</description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 <token name="@OPERATION@">RELAX</token>
8 <token name="@operation@">relax</token>
9 </macros> 7 </macros>
10 <expand macro="requirements"/> 8 <expand macro="requirements"/>
11 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
12 @SYMLINK_FILES@ 10 @SYMLINK_FILES@
13 export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" && 11 export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" &&
14 hyphy relax 12 hyphy relax
15 --alignment ./$input_file 13 --alignment ./$input_file
16 #if $input_nhx: 14 @INPUT_TREE@
17 --tree ./input.nhx 15 --models '$models'
16 --code '$gencodeid'
17 --test '$test'
18 #if $reference:
19 --reference '$reference'
18 #end if 20 #end if
19 --models '$analysisType' 21 @advanced_options@
20 --code '$gencodeid' 22 --output '$relax_output'
21 #if $treeAnnotations == "2": 23 @ERRORS@
22 --test TEST
23 --reference REFERENCE
24 #else:
25 --test TEST
26 #end if
27 > '$relax_log' ;
28 @CATCH_ERROR@
29 ]]></command> 24 ]]></command>
30 <inputs> 25 <inputs>
31 <expand macro="inputs"/> 26 <expand macro="inputs"/>
32 <expand macro="gencode"/> 27 <expand macro="gencode"/>
33 <param argument="--model" name="analysisType" type="select" label="Analysis Type" > 28 <param argument="--models" type="select" label="Analysis Type" >
34 <option value="All">All</option> 29 <option value="All">All</option>
35 <option value="Minimal">Minimal</option> 30 <option value="Minimal">Minimal</option>
36 </param> 31 </param>
37 <param name="treeAnnotations" type="select" label="Tree Annotations" help = "Is there one or two sets of annotated branches in the Newick file?"> 32 <param argument="--test" type="text" value="Unlabeled branches" optional="false" label="Branches to use as the test set">
38 <option value="1">TEST only</option> 33 <sanitizer invalid_char="">
39 <option value="2">TEST and REFERENCE</option> 34 <valid initial="default" />
35 </sanitizer>
40 </param> 36 </param>
37 <param argument="--reference" type="text" optional="true" label="Branches to use as the reference set">
38 <sanitizer invalid_char="">
39 <valid initial="default" />
40 </sanitizer>
41 </param>
42 <expand macro="srv" />
41 </inputs> 43 </inputs>
42 <outputs> 44 <outputs>
43 <data name="relax_log" format="txt"/>
44 <data name="relax_output" format="hyphy_results.json"/> 45 <data name="relax_output" format="hyphy_results.json"/>
46 <expand macro="alternative_model_output" />
45 </outputs> 47 </outputs>
46 <tests> 48 <tests>
47 <test> 49 <test>
48 <param name="input_file" ftype="fasta" value="relax-in1.fa"/> 50 <param name="input_file" ftype="fasta" value="relax-in1.fa"/>
49 <param name="input_nhx" ftype="nhx" value="relax-in1.nhx"/> 51 <param name="input_nhx" ftype="nhx" value="relax-in1.nhx"/>
52 <param name="test" value="TEST" />
50 <output name="relax_output" file="relax-out1.json" compare="sim_size"/> 53 <output name="relax_output" file="relax-out1.json" compare="sim_size"/>
54 </test>
55 <test>
56 <param name="input_file" ftype="nex" value="relax-in2.nex"/>
57 <param name="srv_options" value="specify" />
58 <param name="save_alternative_model" value="true" />
59 <param name="test" value="PR" />
60 <param name="srv" value="Yes" />
61 <output name="relax_output" file="relax-out2-1.json" compare="sim_size"/>
62 <output name="alternative_model" file="relax-out2-2.json" compare="sim_size"/>
51 </test> 63 </test>
52 </tests> 64 </tests>
53 <help><![CDATA[ 65 <help><![CDATA[
54 RELAX: a test for selection differences 66 RELAX: a test for selection differences
55 ======================================= 67 =======================================