Mercurial > repos > iuc > hyphy_meme
comparison hyphy_meme.xml @ 25:4e25db2c3070 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
| author | iuc |
|---|---|
| date | Tue, 27 Apr 2021 17:45:03 +0000 |
| parents | dff11b7c9745 |
| children | d4ec17544e6b |
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| 24:c95c493ad5fa | 25:4e25db2c3070 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy1" profile="19.09"> | 2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy2" profile="19.09"> |
| 3 <description>Mixed Effects Model of Evolution</description> | 3 <description>Mixed Effects Model of Evolution</description> |
| 4 <macros> | 4 <macros> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 <token name="@OPERATION@">MEME</token> | |
| 7 <token name="@operation@">meme</token> | |
| 8 </macros> | 6 </macros> |
| 9 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
| 10 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 11 @SYMLINK_FILES@ | 9 @SYMLINK_FILES@ |
| 12 @HYPHYMPI@ meme | 10 @HYPHYMPI@ meme |
| 13 --alignment ./$input_file | 11 --alignment ./$input_file |
| 14 #if $input_nhx: | 12 @INPUT_TREE@ |
| 15 --tree ./input.nhx | |
| 16 #end if | |
| 17 --code '$gencodeid' | 13 --code '$gencodeid' |
| 18 --branches '$branches' | 14 @branch_options@ |
| 19 --pvalue '$p_value' | 15 --pvalue '$p_value' |
| 20 --output '$meme_output' | 16 --output '$meme_output' |
| 21 --full-model '$full_model' | 17 --full-model '$full_model' |
| 22 > '$meme_log' | 18 @ERRORS@ |
| 23 ; | |
| 24 @CATCH_ERROR@ | |
| 25 ]]></command> | 19 ]]></command> |
| 26 <inputs> | 20 <inputs> |
| 27 <expand macro="inputs"/> | 21 <expand macro="inputs"/> |
| 28 <expand macro="gencode"/> | 22 <expand macro="gencode"/> |
| 29 <expand macro="branches"/> | 23 <expand macro="branches"/> |
| 30 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/> | 24 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/> |
| 31 <param argument="--full-model" type="boolean" truevalue="Yes" falsevalue="No" label="Perform branch length re-optimization under the full codon model" /> | 25 <param argument="--full-model" type="boolean" truevalue="Yes" falsevalue="No" label="Perform branch length re-optimization under the full codon model" /> |
| 32 </inputs> | 26 </inputs> |
| 33 <outputs> | 27 <outputs> |
| 34 <data name="meme_log" format="txt"/> | |
| 35 <data name="meme_output" format="hyphy_results.json" /> | 28 <data name="meme_output" format="hyphy_results.json" /> |
| 36 </outputs> | 29 </outputs> |
| 37 <tests> | 30 <tests> |
| 38 <test> | 31 <test> |
| 39 <param name="input_file" ftype="fasta" value="meme-in1.fa"/> | 32 <param name="input_file" ftype="fasta" value="meme-in1.fa"/> |