Mercurial > repos > edward-kirton > minimus2
annotate minimus2/minimus2.xml @ 0:937ba44abdb7 default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | edward-kirton |
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date | Tue, 07 Jun 2011 17:29:43 -0400 |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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1 <tool id="minimus2" name="Minimus2" version='1.0.1'> |
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2 <description>Merge two sets of assembled contig sequences</description> |
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3 <command interpreter='perl'>minimus2_wrapper.pl -tmpdir $contigs_outfile.extra_files_path $infile1 $infile2 $contigs_outfile $singletons_outfile |
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4 #if $prefix1.select == 'y': |
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5 -prefix1 $prefix1.prefix |
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6 #end if |
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7 #if $prefix2.select == 'y': |
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8 -prefix2 $prefix2.prefix |
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9 #end if |
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10 </command> |
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11 <inputs> |
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12 <param name="infile1" type="data" format="fasta" label="Contig sequences file 1"/> |
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13 <conditional name='prefix1'> |
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14 <param name='select' type='select' label='Rename contigs in file 1 by adding prefix?'> |
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15 <option value='y'>yes, add prefix</option> |
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16 <option value='n'>no, contig IDs are unique</option> |
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17 </param> |
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18 <when value='y'> |
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19 <param name="prefix" type="text" value="1" label="Prefix for sequences in file 1" /> |
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20 </when> |
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21 <when value='n'> |
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22 </when> |
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23 </conditional> |
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24 <param name="infile2" type="data" format="fasta" label="Contig sequences file 2"/> |
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25 <conditional name='prefix2'> |
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26 <param name='select' type='select' label='Rename contigs in file 2 by adding prefix?'> |
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27 <option value='y'>yes, add prefix</option> |
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28 <option value='n'>no, contig IDs are unique</option> |
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29 </param> |
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30 <when value='y'> |
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31 <param name="prefix" type="text" value="2" label="Prefix for sequences in file 2" /> |
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32 </when> |
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33 <when value='n'> |
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34 </when> |
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35 </conditional> |
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36 </inputs> |
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37 <outputs> |
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38 <data name="contigs_outfile" format="fasta" label="contigs" /> |
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39 <data name="singletons_outfile" format="fasta" label="singletons" /> |
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40 </outputs> |
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41 <help> |
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42 **What it does** |
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43 |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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44 minimus2 is part of the AMOS assembler package, designed for merging one or two sets of contig sequences. |
937ba44abdb7
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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45 |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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46 This tool preprocesses the Fasta input files prior to coassembly with minimus2 and separately returns the new contigs |
937ba44abdb7
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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47 and the sequences which did not co-assemble (singletons). |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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48 |
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49 The input sequences in each dataset must have unique IDs; use of the optional rename with prefix option avoids this. |
937ba44abdb7
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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50 |
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51 **Documentation** |
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52 |
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53 http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus2 |
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54 </help> |
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55 </tool> |