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"planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/uvp commit d0b060e7d9cc9fd89926dbc07fc93c8a1471b3fe-dirty"
author dfornika
date Mon, 28 Oct 2019 18:36:17 -0400
parents 679d120f8c09
children
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1 <tool id="uvp" name="Unified Variant analysis Pipeline for M. tuberculosis complex" version="@TOOL_VERSION@+galaxy0">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">uvp</requirement>
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8 </requirements>
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9 <version_command>uvp --version</version_command>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
3
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12 #if $single_paired.single_paired_selector == 'yes'
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13 ln -s '${single_paired.forward_input}' 'R1.fastq.gz' &&
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14 ln -s '${single_paired.reverse_input}' 'R2.fastq.gz' &&
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15 #elif $single_paired.single_paired_selector == "collection":
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16 ln -s '${single_paired.input_pair.forward}' 'R1.fastq.gz' &&
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17 ln -s '${single_paired.input_pair.reverse}' 'R2.fastq.gz' &&
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18 #else:
4
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19 ln -s '${single_paired.input_sequences}' 'R1.fastq.gz' &&
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20 #end if
0
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21 uvp
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22 --threads \${GALAXY_SLOTS:-1}
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23 --verbose
0
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24 #if $single_paired.single_paired_selector == 'yes'
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25 -n 'sample'
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26 -q 'R1.fastq.gz'
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27 -q2 'R2.fastq.gz'
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28 #elif $single_paired.single_paired_selector == "collection":
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29 -n 'sample'
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30 -q 'R1.fastq.gz'
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31 -q2 'R2.fastq.gz'
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32 #else:
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33 -n 'sample'
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34 -q 'R1.fastq.gz'
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35 #end if
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36 --krakendb '${kraken_database.fields.path}'
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37 -r '${reference}'
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38 ${annotate}
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39 ]]>
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40 </command>
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41 <inputs>
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42 <conditional name="single_paired">
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43 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
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44 <option value="collection">Collection</option>
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45 <option value="yes">Paired</option>
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46 <option selected="True" value="no">Single</option>
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47 </param>
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48 <when value="collection">
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49 <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
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50 </when>
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51 <when value="yes">
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52 <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
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53 <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
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54 </when>
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55 <when value="no">
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56 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
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57 </when>
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58 </conditional>
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59 <param name="kraken_database" type="select">
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60 <options from_data_table="kraken_databases">
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61 <validator type="no_options" message="No Kraken databases are available" />
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62 </options>
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63 </param>
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64 <param name="reference" type="data" format="fasta" label="Reference Sequence" />
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65 <param name="annotate" type="boolean" truevalue="--annotate" falsevalue="" />
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66 </inputs>
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67 <outputs>
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68 <data name="lineage_report" label="Lineage Report" format="tabular" from_work_dir="Results/sample/sample.lineage_report.txt"/>
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69 <data name="validation_report" label="Validation Report" format="tabular" from_work_dir="Results/sample/validation/Validation_report.txt"/>
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70 <data name="kraken_report" label="Kraken Report" format="tabular" from_work_dir="Results/sample/kraken/final_report.txt"/>
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71 <data name="low_quals" label="Low-quality" format="tabular" from_work_dir="QC/low_quals.txt"/>
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72 </outputs>
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73 <tests>
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74 </tests>
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75 <help>
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76 <![CDATA[
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77 ]]>
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78 </help>
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79 <expand macro="citations" />
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80 </tool>