Mercurial > repos > iuc > hyphy_gard
diff hyphy_gard.xml @ 23:a0731e81e0c2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
| author | iuc |
|---|---|
| date | Tue, 20 Apr 2021 10:25:18 +0000 |
| parents | 42efcb0955e6 |
| children | 1fb98a84e86d |
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--- a/hyphy_gard.xml Fri Apr 09 21:48:33 2021 +0000 +++ b/hyphy_gard.xml Tue Apr 20 10:25:18 2021 +0000 @@ -3,12 +3,15 @@ <description>Genetic Algorithm for Recombination Detection</description> <macros> <import>macros.xml</import> + <token name="@OPERATION@">GARD</token> + <token name="@operation@">gard</token> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - ln -s '$input_file' gard_input.fa && + ln -s '$input_file' input.$input_file.extension && + #set $input_file = 'input.%s' % $input_file.extension @HYPHYMPI@ gard - --alignment ./gard_input.fa + --alignment ./$input_file --type '$datatype.value' #if str($datatype.value) == 'codon': --code '$datatype.gencodeid' @@ -23,10 +26,10 @@ --output-lf '$gard_output' > '$gard_log' ; - @CATCH_MPIERR@ + @CATCH_ERROR@ ]]></command> <inputs> - <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> + <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" /> <conditional name="datatype"> <param argument="--type" name="value" type="select" label="Alignment kind"> <option value="nucleotide">Nucleotide</option> @@ -64,7 +67,7 @@ <tests> <test> <param name="input_file" ftype="fasta" value="gard-in1.fa"/> - <output name="gard_output" file="gard-out1.nex" compare="sim_size" delta="160000"/> + <output name="gard_output" file="gard-out1.nex" compare="sim_size"/> </test> </tests> <help><![CDATA[