Mercurial > repos > iuc > lorikeet_spoligotype
annotate lorikeet.xml @ 2:da22667725c7 draft default tip
planemo upload for repository https://github.com/AbeelLab/lorikeet commit 20b560d28599c597257dbc77f8f38217cd61ae46
author | iuc |
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date | Tue, 12 Mar 2024 11:22:08 +0000 |
parents | f9c37d0b3002 |
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rev | line source |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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1 <tool id="lorikeet_spoligotype" name="lorikeet spoligotyping" version="@TOOL_VERSION@+galaxy0" profile="17.01"> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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2 <description>M. tuberculosis DNA fingerprinting</description> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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3 |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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4 <macros> |
1
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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5 <token name="@TOOL_VERSION@">20</token> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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6 </macros> |
2
da22667725c7
planemo upload for repository https://github.com/AbeelLab/lorikeet commit 20b560d28599c597257dbc77f8f38217cd61ae46
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7 <xrefs> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 20b560d28599c597257dbc77f8f38217cd61ae46
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8 <xref type="bio.tools">lorikeet</xref> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 20b560d28599c597257dbc77f8f38217cd61ae46
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9 </xrefs> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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10 <requirements> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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11 <requirement type="package" version="@TOOL_VERSION@">lorikeet</requirement> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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12 </requirements> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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13 |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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14 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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15 #set $input_file = 'input.' + $input.extension |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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16 ln -s '${input}' $input_file && |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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17 lorikeet spoligotype |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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18 -o '${output_txt}' |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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19 $input_file |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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20 #if $spacer_source.source_type == 'file': |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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21 -s '${spacer_source.spacer}' |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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22 #end if |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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23 ]]> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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24 </command> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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25 <inputs> |
1
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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26 <param name="input" label="Input sequences" type="data" format="bam,fastq,fastq.gz" help="Reads of sample(s) being spoligotyped" /> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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27 <conditional name="spacer_source"> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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28 <param type="select" name="source_type" label="Source for spacer sequences"> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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29 <option selected="true" value="builtin">Built-in</option> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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30 <option value="file">File with custom spacers</option> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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31 </param> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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32 <when value="builtin"> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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33 </when> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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34 <when value="file"> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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35 <param argument="--spacer" type="data" format="fasta" label="Spacer file" help="FASTA format file containing customer spacer library" /> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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36 </when> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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37 </conditional> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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38 </inputs> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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39 <outputs> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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40 <data name="output_txt" format="txt" label="Spoligotype on ${on_string}" /> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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41 </outputs> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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42 <tests> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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43 <test> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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44 <param name="input" value="input.bam" ftype="bam" /> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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45 <output name="output_txt"> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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46 <assert_contents> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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47 <has_text text="1111111111 1111111011 1111111111 1100001111 111" /> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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48 </assert_contents> |
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49 </output> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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50 </test> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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51 <test> |
1
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52 <param name="input" value="input.fastq" ftype="fastq" /> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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53 <output name="output_txt"> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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54 <assert_contents> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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55 <has_text text="1111111111 1111111011 1111111111 1100001111 111" /> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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56 </assert_contents> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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57 </output> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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58 </test> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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59 <test> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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60 <param name="input" value="input.fastq.gz" ftype="fastq.gz" /> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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61 <output name="output_txt"> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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62 <assert_contents> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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63 <has_text text="1111111111 1111111011 1111111111 1100001111 111" /> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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64 </assert_contents> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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65 </output> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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66 </test> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
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67 <test> |
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68 <param name="input" value="input.bam" ftype="bam" /> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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69 <param name="source_type" value="file" /> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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70 <param name="spacer" value="custom_spacers.fasta" ftype="fasta" /> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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71 <output name="output_txt"> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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72 <assert_contents> |
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73 <has_text text="1111111111 0000000000 0000000000 0000000000 000" /> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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74 </assert_contents> |
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75 </output> |
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76 </test> |
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77 </tests> |
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78 <help><![CDATA[ |
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79 Lorikeet_ is a tool for digital spoligotyping_ of M. tuberculosis strains |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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80 from Illumina data. Input is a file of Illumina reads and output is |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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81 a spoligotyping report. |
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82 |
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83 While by default lorikeet uses its own built-in collection of spacer |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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84 sequences, a custom file of spacers can be provided if necessary. |
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85 |
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86 .. _Lorikeet: https://github.com/AbeelLab/lorikeet |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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87 .. _spoligotyping: https://link.springer.com/protocol/10.1007%2F978-1-60327-999-4_10 |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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88 ]]> |
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89 </help> |
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90 <citations> |
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91 <citation type="doi">10.1371/journal.pmed.1001880</citation> |
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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92 </citations> |
d35cc8e07d00
planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
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parents:
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93 </tool> |