Mercurial > repos > iuc > lorikeet_spoligotype

annotate lorikeet.xml @ 0:d35cc8e07d00 draft

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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
author iuc
date Tue, 08 May 2018 04:23:01 -0400
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children f9c37d0b3002
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d35cc8e07d00 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">
d35cc8e07d00 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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4 <macros>
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5 <token name="@TOOL_VERSION@">17</token>
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6 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">lorikeet</requirement>
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10 </requirements>
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11
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12 <command detect_errors="exit_code"><![CDATA[
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13 #set $input_file = 'input.' + $input.extension
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14 ln -s '${input}' $input_file &&
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15 lorikeet spoligotype
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16 -o '${output_txt}'
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17 $input_file
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18 #if $spacer_source.source_type == 'file':
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19 -s '${spacer_source.spacer}'
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20 #end if
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="input" label="Input sequences" type="data" format="bam" help="Reads of sample(s) being spoligotyped" />
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25 <conditional name="spacer_source">
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26 <param type="select" name="source_type" label="Source for spacer sequences">
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27 <option selected="true" value="builtin">Built-in</option>
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28 <option value="file">File with custom spacers</option>
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29 </param>
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30 <when value="builtin">
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31 </when>
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32 <when value="file">
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33 <param argument="--spacer" type="data" format="fasta" label="Spacer file" help="FASTA format file containing customer spacer library" />
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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="output_txt" format="txt" label="Spoligotype on ${on_string}" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input" value="input.bam" ftype="bam" />
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43 <output name="output_txt">
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44 <assert_contents>
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45 <has_text text="1111111111 1111111011 1111111111 1100001111 111" />
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46 </assert_contents>
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47 </output>
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48 </test>
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49 <test>
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50 <param name="input" value="input.bam" ftype="bam" />
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51 <param name="source_type" value="file" />
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52 <param name="spacer" value="custom_spacers.fasta" ftype="fasta" />
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53 <output name="output_txt">
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54 <assert_contents>
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55 <has_text text="1111111111 0000000000 0000000000 0000000000 000" />
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56 </assert_contents>
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57 </output>
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 Lorikeet_ is a tool for digital spoligotyping_ of M. tuberculosis strains
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62 from Illumina data. Input is a file of Illumina reads and output is
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63 a spoligotyping report.
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64
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65 While by default lorikeet uses its own built-in collection of spacer
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66 sequences, a custom file of spacers can be provided if necessary.
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67
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68 .. _Lorikeet: https://github.com/AbeelLab/lorikeet
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69 .. _spoligotyping: https://link.springer.com/protocol/10.1007%2F978-1-60327-999-4_10
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70 ]]>
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71 </help>
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72 <citations>
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73 <citation type="doi">10.1371/journal.pmed.1001880</citation>
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74 </citations>
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75 </tool>