Mercurial > repos > ktnyt > gembassy
diff glang-galaxy-conf/kbws/ktrnascan_se.xml @ 2:8947fca5f715 draft default tip
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author | ktnyt |
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date | Fri, 26 Jun 2015 05:21:44 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glang-galaxy-conf/kbws/ktrnascan_se.xml Fri Jun 26 05:21:44 2015 -0400 @@ -0,0 +1,64 @@ +<tool id="EMBOSS: ktrnascan_se" name="ktrnascan_se" version="1.0.2"> + <description>Finds tRNA genes using tRNAscan-SE</description> + <command>ktrnascan_se -seqall $input1 -title $title -mode $mode -source $source -gcode $gcode -pesudogene $pesudogene -origin $origin -ace $ace -codons $codons -fpos $fpos -breakdown $breakdown -covescore $covescore -euparams $euparams -euscore $euscore -auto -outfile $out_file1</command> + <inputs> + <param format="data" name="input1" type="data"> + <label>Sequence</label> + </param> + <param name="title" size="4" type="text" value=""> + <label>Title of your job</label> + </param> + <param name="mode" size="4" type="text" value="Default"> + <label>Search mode</label> + </param> + <param name="source" size="4" type="text" value="Mixed (general tRNA model)"> + <label>Training data set</label> + </param> + <param name="gcode" size="4" type="text" value="Universal"> + <label>Genetic Code for tRNA Isotype Prediction</label> + </param> + <param name="pesudogene" type="select" value=""> + <label>Disable pseudo gene checking</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="origin" type="select" value=""> + <label>Show origin of first-pass hits</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="ace" type="select" value=""> + <label>Display results in ACeDB format</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="codons" type="select" value=""> + <label>Show codons instead of tRNA anticodons</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="fpos" type="select" value=""> + <label>Show false positives from tRNAscan/EufindtRNA</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="breakdown" type="select" value=""> + <label>Show primary and secondary structure components to Cove scores</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="covescore" size="4" type="text" value=""> + <label>Cove score cutoff</label> + </param> + <param name="euparams" size="4" type="text" value="Default"> + <label>EufindtRNA search parameters</label> + </param> + <param name="euscore" size="4" type="text" value=""> + <label>Intermediate score cutoff</label> + </param> + + </inputs> + <outputs> + <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" /> + </outputs> +</tool>