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annotate seqtk_mergefa.xml @ 4:ecf1c30da3a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
author iuc
date Wed, 17 Oct 2018 05:59:21 -0400
parents bc7d99f46a5d
children a09586d5149a
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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[
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10 seqtk mergefa
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11 -q $q
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12 $i
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13 $m
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14 $r
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15 $h
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16 '$in_fa1'
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17 '$in_fa2'
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18 #echo "| gzip --no-name" if $in_fa1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
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19 ]]></command>
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20 <inputs>
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21 <param name="in_fa1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
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22 <param name="in_fa2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #2"/>
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23 <param argument="-q" type="integer" value="0" label="Quality threshold"/>
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24 <param argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Take intersection" />
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25 <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Convert to lowercase when one of the input base is N" />
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26 <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Pick a random allele from het" />
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27 <param argument="-h" type="boolean" truevalue="-h" falsevalue="" checked="false" label="Suppress hets in the input" />
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28 </inputs>
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29 <outputs>
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30 <data name="default" format_source="in_fa1" label="Merger of $in_fa1.name and $in_fa2.name"/>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="in_fa1" value="seqtk_mergefa1.fa"/>
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35 <param name="in_fa2" value="seqtk_mergefa2.fa"/>
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36 <output name="default" file="seqtk_mergefa.out" ftype="fasta"/>
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37 </test>
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38 <test>
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39 <param name="in_fa1" value="seqtk_mergefa1.fa"/>
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40 <param name="in_fa2" value="seqtk_mergefa2.fa"/>
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41 <param name="m" value="True" />
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42 <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/>
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43 </test>
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44 <test>
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45 <param name="in_fa1" value="seqtk_mergefa1.fa.gz" ftype="fasta.gz"/>
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46 <param name="in_fa2" value="seqtk_mergefa2.fa.gz" ftype="fasta.gz"/>
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47 <param name="m" value="True" />
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48 <output name="default" file="seqtk_mergefa2.out.gz" ftype="fasta.gz"/>
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52 **What it does**
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53
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54 Merges two fasta files, using ambiguity codes
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55
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56 ::
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57
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58 # seq1.fa
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59 >test0
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60 ACTGACTGAAA
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61
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62 # seq2.fa
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63 >test0
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64 ACTGAMTGCGN
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65
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66 In the following the `-m` option has been set to highlight seqtk-mergefa's features.
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67
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68 ::
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69
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70 >test0
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71 ACTGACTGxxa
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72
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73 @ATTRIBUTION@
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74 ]]></help>
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75 <expand macro="citation" />
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76 </tool>