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1 <tool id="vsearch_alignment" name="VSearch alignment" version="@VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>vsearch_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command>
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10 <![CDATA[
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11 vsearch
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12 @GENERAL@
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13 $acceptall
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14 --id $id
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15 --iddef $iddef
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16 --allpairs_global "$infile"
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17 --alnout $outfile
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18 --query_cov $query_cov
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19 @USERFIELDS@
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20 ]]>
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21 </command>
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22 <inputs>
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23 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--allpairs_global)" />
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24 <expand macro="id_and_iddef" />
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25 <param name="acceptall" type="boolean" truevalue="--acceptall" falsevalue="" checked="False"
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26 label="Output all pairwise alignments" help="This option overrides all other accept/reject options including identity. (--acceptall)"/>
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27 <param name="query_cov" type="float" value="" optional="True" label="Reject if fraction of query seq. aligned lower than this value"
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28 help="(--query_cov)"/>
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29 <expand macro="userfields" />
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30 </inputs>
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31 <outputs>
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32 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="infile" value="Rfam_11_0.repr.fasta.bz2" ftype="fasta" />
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37 <param name="acceptall" value=""/>
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38 <param name="id" value="0.97"/>
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39 <param name="query_cov" value="0.95"/>
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40 <param name="userfields" value="query,target"/>
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41 <output name="outfile" file="alignment_result1.fasta" lines_diff="4" ftype="fasta" />
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42 </test>
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43 </tests>
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44 <help>
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45 <![CDATA[
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46 **What it does**
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47
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48 Pairwise alignments of all sequences.
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49
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50
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51 Alignment options (most searching options also apply)
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52 --allpairs_global FILENAME perform global alignment of all sequence pairs
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53 --alnout FILENAME filename for human-readable alignment output
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54 --acceptall output all pairwise alignments
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55
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56 @EXTERNAL_DOCUMENTATION@
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57
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58 -------
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59
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60 @REFERENCES@
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61
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62
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63 ]]>
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64 </help>
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65 <expand macro="citations" />
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66 </tool>
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