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Update Orione citation. Add <citations> tag. Use package_muscle_3_8_31 from iuc.
author crs4
date Thu, 04 Jun 2015 11:34:04 -0400
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533b3b2a1e66 Update Orione citation. Add <citations> tag. Use package_muscle_3_8_31 from iuc.
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1 <tool id="muscle" name="MUSCLE" version="0.0.11">
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2 <description>multiple aligner</description>
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3 <requirements>
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4 <requirement type="package" version="3.8.31">muscle</requirement>
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533b3b2a1e66 Update Orione citation. Add &lt;citations&gt; tag. Use package_muscle_3_8_31 from iuc.
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5 <requirement type="set_environment">FASTA_MAX_SIZE</requirement>
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6 </requirements>
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7 <version_command>muscle -version</version_command>
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8 <command>
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9 FASTA_MAX_SIZE=\${FASTA_MAX_SIZE:-100000};
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10 if [ `stat -c "%s" $multifasta` -gt \$FASTA_MAX_SIZE ]; then echo "Multi-FASTA file is bigger than the configured limit for MUSCLE (\$FASTA_MAX_SIZE bytes)." >&amp;2; exit 1; fi;
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11 muscle -quiet -in $multifasta -out $output -log $log
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12 #if str($maxiters)
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13 -maxiters $maxiters
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14 #end if
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15 #if $diags
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16 -diags
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17 #end if
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18 </command>
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19 <inputs>
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20 <param name="multifasta" type="data" format="fasta" label="Multi-FASTA file" />
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21 <param name="maxiters" type="integer" value="2" min="1" max="16" optional="true" label="Maximum number of iterations to run (-maxiters)" help="Set to 2 for large datasets where refinement (iterations 3+) is too slow." />
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22 <param name="diags" type="boolean" label="Diagonal optimization (-diags)" help="Speed up the algorithm, especially for closely related sequences, at the expense of some reduction in accuracy" />
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23 </inputs>
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24 <outputs>
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25 <data name="output" format="fasta" label="${tool.name} on ${on_string}: aligned sequences"/>
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26 <data name="log" format="txt" label="${tool.name} on ${on_string}: log"/>
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27 </outputs>
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533b3b2a1e66 Update Orione citation. Add &lt;citations&gt; tag. Use package_muscle_3_8_31 from iuc.
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28 <tests>
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29 </tests>
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30 <help>
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31 **What it does**
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32
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33 This tool performs multiple sequence alignment using MUSCLE.
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34
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35 **License and citation**
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36
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533b3b2a1e66 Update Orione citation. Add &lt;citations&gt; tag. Use package_muscle_3_8_31 from iuc.
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37 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
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38
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39 .. _CRS4 Srl.: http://www.crs4.it/
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40 .. _MIT license: http://opensource.org/licenses/MIT
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41
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533b3b2a1e66 Update Orione citation. Add &lt;citations&gt; tag. Use package_muscle_3_8_31 from iuc.
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42 You can use this tool only if you agree to the license terms of: `MUSCLE`_.
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43
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44 .. _MUSCLE: http://drive5.com/muscle/
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46 If you use this tool, please cite:
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48 - |Cuccuru2014|_
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49 - |Edgar2004|_.
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51 .. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
533b3b2a1e66 Update Orione citation. Add &lt;citations&gt; tag. Use package_muscle_3_8_31 from iuc.
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52 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
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53 .. |Edgar2004| replace:: Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. *Nucleic Acids Res.* 32(5), 1792-1797
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54 .. _Edgar2004: http://nar.oxfordjournals.org/content/32/5/1792
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55 </help>
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56 <citations>
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57 <citation type="doi">10.1093/nar/gkh340</citation>
533b3b2a1e66 Update Orione citation. Add &lt;citations&gt; tag. Use package_muscle_3_8_31 from iuc.
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58 </citations>
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59 </tool>