Mercurial > repos > bgruening > rnaz_cluster
diff rnazCluster.xml @ 0:d21d8e70e802 draft default tip
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 04:14:06 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnazCluster.xml Wed Jan 30 04:14:06 2019 -0500 @@ -0,0 +1,61 @@ +<tool id="rnaz_cluster" name="RNAz Cluster" version="2.1"> + <requirements> + <requirement type="package" version="2.1">rnaz</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + rnazCluster.pl + --cutoff $cutoff + $window_or_loci + #if $header: + $header + #end if + '$input' + > '$output' + ]]></command> + <inputs> + <param type="data" name="input" format="text" /> + <param argument="--cutoff" type="float" value="0.5" label="Only consider hits with RNAz class probality P>cutoff" /> + <param name="window_or_loci" type="select" label="Print information for window or loci"> + <option value="--windows">Print information for windows only</option> + <option value="--loci">Print information for loci only</option> + </param> + <param argument="--header" type="boolean" checked="true" truevalue="--header" falsevalue="" label="Print a header explaining the fields of the output" /> + </inputs> + <outputs> + <data name="output" format="data"/> + </outputs> + <tests> + <test> + <param name="input" value="unknown.rnaz"/> + <param name="cutoff" value="0"/> + <output name="output" file="unknown.rnaz.clustered"/> + </test> + <test> + <param name="input" value="tRNA.rnaz"/> + <param name="window_or_loci" value="loci"/> + <output name="output" file="tRNA.rnaz.clustered"/> + </test> + </tests> + <help><![CDATA[ + + Clusters RNAz windows back into overlapping loci. + + Usage: rnazCluster.pl [options] [file] + + Options: -c X, --cutoff=X Only consider hits with RNAz class + probablility P > X (Default:0.5) + + -w, --windows -l, --loci Set these flags to print information for + windows and/or loci in the output. By default, both single windows + and combined loci are printed. + + -d, --header Print a header explaining the fields of the output + (see below for a detailed description of the fields). + + ]]></help> + + <citations> + <citation type="doi">10.1142/9789814295291_0009</citation> + </citations> + +</tool>