Mercurial > repos > iuc > hyphy_relax
comparison hyphy_relax.xml @ 25:a4c5dc437558 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author | iuc |
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date | Tue, 27 Apr 2021 18:03:51 +0000 |
parents | 801547975424 |
children | 3415a580926d |
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24:098451b762fb | 25:a4c5dc437558 |
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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 ======================================= |