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1 <tool id="galru" name="galru" version="@VERSION@">
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2 <description>Long read spoligotyping for Mycobacterium tuberculosis</description>
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3 <macros>
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4 <token name="@VERSION@">1.0.0</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">galru</requirement>
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8 </requirements>
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9 <version_command>galru --version</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 galru
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12 --technology $technology
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13 #if str($cas_input.cas_select) == "history":
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14 --cas_fasta '$cas_input.cas_file'
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15 #end if
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16 --gene_start_offset $gene_start_offset
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17 --min_mapping_quality $min_mapping_quality
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18 --qcov_margin $qcov_margin
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19 --min_bitscore $min_bitscore
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20 --min_identity $min_identity
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21 --threads \${GALAXY_SLOTS:-4}
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22 $extended
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23 $debug
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24 $verbose
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25 --output_file $output
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26 $fastq
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27 ]]> </command>
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28
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29 <inputs>
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30 <param name="fastq" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="Uncorrected long reads"/>
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31 <conditional name="cas_input">
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32 <param name="cas_select" type="select" label="CAS file">
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33 <option selected="true" value="bundle">Use bundled CAS file</option>
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34 <option value="history">Use a fasta file in the history</option>
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35 </param>
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36 <when value="history">
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37 <param name="cas_file" type="data" format="fasta,fasta.gz" label="Select a CAS file"/>
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38 </when>
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39 </conditional>
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40 <param name="technology" type="select" optional="false" label="Sequencing technology">
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41 <option value="map-ont">map-ont</option>
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42 <option value="map-pb">map-pb</option>
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43 <option value="ava-ont">ava-ont</option>
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44 <option value="ava-pb">ava-pb</option>
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45 </param>
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46 <param name="extended" argument="--extended_results" type="boolean" truevalue="--extended_results" falsevalue="" checked="false" label="Output extended results" />
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47 <param name="gene_start_offset" argument="--gene_start_offset" type="integer" min="0" value="30" label="Only count CRISPR reads which cover this base"/>
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48 <param name="min_mapping_quality" argument="--min_mapping_quality" type="integer" min="0" value="10" label="Minimum mapping quality score"/>
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49 <param name="qcov_margin" argument="--qcov_margin" type="integer" min="0" value="100" label="Maximum perc coverage difference between CRISPR and read"/>
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50 <param name="min_bitscore" argument="--min_bitscore" type="integer" min="0" value="38" label="Minimum blast bitscore"/>
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51 <param name="min_identity" argument="--min_identity" type="integer" min="0" value="95" label="Minimum blast identity"/>
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52 <param name="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Turn on debugging" />
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53 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Turn on verbose output" />
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54 </inputs>
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55 <outputs>
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56 <data name="output" format="tabular" label="${tool.name} on ${on_string} Output"/>
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57 <data name="log" format="text" label="${tool.name} on ${on_string} Log">
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58 <filter>debug is True</filter>
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59 </data>
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60 </outputs>
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61
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62 <help><![CDATA[
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63
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64 Documentation can be found at `<https://github.com/quadram-institute-bioscience/galru>`_.
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65
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66 ]]> </help>
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67 <citations>
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68 <citation type="doi">10.1101/2020.05.31.126490v1</citation>
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69 </citations>
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70 </tool>
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