Mercurial > repos > ktnyt > gembassy
diff glang-galaxy-conf/kbws/kmafft.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/kmafft.xml Fri Jun 26 05:21:44 2015 -0400 @@ -0,0 +1,44 @@ +<tool id="EMBOSS: kmafft" name="kmafft" version="1.0.2"> + <description>Multiple sequence alignment using MAFFT</description> + <command>kmafft -seqall $input1 -strategy $strategy -outorder $outorder -opengap $opengap -ep $ep -scorematrix $scorematrix -homologs $homologs -showhomologs $showhomologs -numhomologs $numhomologs -threshold $threshold -auto -outfile $out_file1</command> + <inputs> + <param format="data" name="input1" type="data"> + <label>Sequence</label> + </param> + <param name="strategy" size="4" type="text" value="auto"> + <label>Calculation strategy.</label> + </param> + <param name="outorder" size="4" type="text" value="aligned"> + <label>Output order. 'input': same as input, 'aligned': aligned</label> + </param> + <param name="opengap" size="4" type="float" value="1.53"> + <label>Gap opening penalty (1.0 - 3.0)</label> + </param> + <param name="ep" size="4" type="float" value="0.0"> + <label>Offset value (0.0 - 1.0)</label> + </param> + <param name="scorematrix" size="4" type="text" value=""> + <label>Scoring matrix. Protein seq: 'BLOSUM30', 'BLOSUM45', 'BLOSUM62'(default), 'BLOSUM80', 'JTT100' or 'JTT200' Nucleotide seq: '1PAM', '20PAM' or '200PAM'(default)</label> + </param> + <param name="homologs" type="select" value="no"> + <label>Collects homologs from SwissProt by BLAST and performs profile-based alignments.</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="showhomologs" type="select" value="no"> + <label>Show homologs sequence</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="numhomologs" size="4" type="integer" value="50"> + <label>Number of homologs sequences</label> + </param> + <param name="threshold" size="4" type="float" value="1e-10"> + <label>Threshold of homologs sequences</label> + </param> + + </inputs> + <outputs> + <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" /> + </outputs> +</tool>