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1 <?xml version="1.0"?>
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2 <tool id="seqtk_mergefa" name="seqtk_mergefa" version="@WRAPPER_VERSION@.0">
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3 <description>merge two FASTA/Q files</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[seqtk mergefa -q $q
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10 $i
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11 $m
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12 $r
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13 $h
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14
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15 $in_fa1
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16 $in_fa2
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17
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18 > $default]]></command>
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19 <inputs>
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20 <param name="in_fa1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
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21 <param name="in_fa2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
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22 <param label="quality threshold" help="(-q)" name="q" type="integer" value="0"/>
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23 <param checked="false" label="take intersection" help="(-i)" name="i" type="boolean" falsevalue="" truevalue="-i"/>
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24 <param checked="false" label="convert to lowercase when one of the input base is N" help="(-m)" name="m" type="boolean" falsevalue="" truevalue="-m"/>
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25 <param checked="false" label="pick a random allele from het" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/>
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26 <param checked="false" label="suppress hets in the input" help="(-h)" name="h" type="boolean" falsevalue="" truevalue="-h"/>
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27 </inputs>
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28 <outputs>
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29 <data format_source="in_fa1" hidden="false" name="default" label="Merger of $in_fa1.name and $in_fa2.name"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="in_fa1" value="seqtk_mergefa1.fa"/>
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34 <param name="in_fa2" value="seqtk_mergefa2.fa"/>
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35 <output name="default" file="seqtk_mergefa.out" ftype="fasta"/>
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36 </test>
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37 <test>
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38 <param name="in_fa1" value="seqtk_mergefa1.fa"/>
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39 <param name="in_fa2" value="seqtk_mergefa2.fa"/>
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40 <param name="m" value="True" />
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41 <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45 **What it does**
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46
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47 Merges two fasta files, using ambiguity codes
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48
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49 ::
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50
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51 # seq1.fa
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52 >test0
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53 ACTGACTGAAA
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54
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55 # seq2.fa
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56 >test0
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57 ACTGAMTGCGN
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58
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59 In the following the `-m` option has been set to highlight seqtk-mergefa's features.
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60
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61 ::
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62
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63 >test0
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64 ACTGACTGxxa
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65
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66 @ATTRIBUTION@
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67 ]]></help>
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68 </tool>
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