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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
author | bgruening |
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date | Wed, 30 Jan 2019 04:13:47 -0500 |
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<tool id="rnaz_select_seqs" name="RNAz Select Seqs" version="2.1"> <requirements> <requirement type="package" version="2.1">rnaz</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ rnazSelectSeqs.pl --num-seqs $numseqs --num-samples $numsamples --opt-id $optid --max-id $maxid #if $noref: --no-ref $noref #end if '$input' > '$output' ]]></command> <inputs> <param format="txt" name="input" type="data" label="Input Alignment File" /> <param argument="--num-seqs" name="numseqs" type="integer" value="6" label="Number of sequences in the output alignment(s). (Default:6)" /> <param argument="--num-samples" name="numsamples" type="integer" value="1" label="Number of output alignments (Default: 1)" /> <param argument="--opt-id" name="optid" type="integer" value="80" label="The resulting alignment(s) is (are) optimized for this value of mean pairwise identity (in percent, default: 80)" /> <param argument="--max-id" name="maxid" type="integer" value="99" label="Sequences from pairs with pairwise identity higher than X% are removed (default: 99, i.e. only almost identical sequences areremoved)" /> <param argument="--no-reference" name="noref" type="boolean" checked="false" truevalue="--no-reference" falsevalue="" label="By default the first sequence (=reference sequence) is always present in the output alignment(s). If you do not care having it removed, set this flag." /> </inputs> <outputs> <data name="output" format="txt" /> </outputs> <tests> <test> <param name="input" value="tRNA.aln"/> <param name="numseqs" value="1"/> <output name="output" file="tRNA_selected.aln"/> </test> </tests> <help><![CDATA[ RNAz up to version 1.0 was limited to alignments of at most 6 sequences. As of version 2.0, there is no limit on the maximum number of sequences. However, under some cirumstances (e.g. for very large alignments) it is still useful to reduce the number of sequences prior to running RNAz. You can select an optimal subset of sequences using rnazSelectSeqs.pl before you put it into RNAz: Usage: rnazSelectSeqs.pl [options] [file] Options: -n N, --num-seqs=N Number of sequences in the output alignment(s). (Default:6) -a N, --num-samples=N Number of output alignments (Default: 1) -i X, --opt-id=X The resulting alignment(s) is (are) optimized for this value of mean pairwise identity (in percent, default: 80) --max-id=X Sequences from pairs with pairwise identity higher than X% are removed (default: 99, i.e. only almost identical sequences are removed) -x, --no-reference By default the first sequence (=reference sequence) is always present in the output alignment(s). If you do not care having it removed, set this flag. -v, --version Prints version information and exits. -h, --help Prints a short help message and exits. --man Prints a detailed manual page and exits. ]]></help> <citations> <citation type="doi">10.1142/9789814295291_0009</citation> </citations> </tool>