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1 <tool id="cfsan-qaqc" name="CFSAN QA/QC process" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="1.65">biopython</requirement>
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4 <requirement type="package" version="1.4.3">matplotlib</requirement>
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5 <requirement type="package" version="1.9.2">numpy</requirement>
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6 <requirement type="package" version="0.16.1">pandas</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #if $reads.reads_select == 'collection'
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10 #set name=$reads.coll.name
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11 #set forward=$reads.coll.forward
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12 #set reverse=$reads.coll.reverse
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13 #else
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14 #set name=$forward.name
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15 #end if
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16 mkdir plots &&
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17 qa_core/gims_core.py --sequencingType "Illumina MiSeq"
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18 --approximateGenomeSize $genomeSize
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19 --coverageThreshold $covThreshold
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20 --minimumQScore $minQ
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21 --output_plots plots
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22 --parallelism \${GALAXY_SLOTS:-6}
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23 --annotate $name
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24 --log -
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25 suite
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26 $forward
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27 $reverse
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28 -o $output
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29 ]]></command>
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30 <inputs>
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31 <conditional name="reads">
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32 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
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33 <option value="collection">Paired collection from your history</option>
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34 <option value="history">Two FASTQ datasets from your history</option>
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35 </param>
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36 <when value="collection">
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37 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
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38 </when>
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39 <when value="history">
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40 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
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41 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
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42 </when>
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43 </conditional>
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44 <param name="genomeSize" type="text" label="Approximate genome size" value="4700000" />
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45 <param name="covThreshold" type="text" label="Coverage threshold" value="20" />
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46 <param name="minQ" type="text" label="Minimum average Q score" value="27.0" />
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47 </inputs>
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48 <outputs>
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49 <data label="QA/QC Results" name="output" format="tabular" />
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50 <data label="Nucleotide plot" name="nucleo_plot" format="png" from_work_dir="nucleotide_distribution.png" />
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51 <data label="QScore Distribution" name="qscore_dist" format="png" from_work_dir="qscore_distribution.png" />
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52 <data label="QScore Histogram" name="qscore_histro" format="png" from_work_dir="qscore_histogram.png" />
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="reads_select" value="collection" />
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57 <param name="coll">
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58 <collection type="list:paired">
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59 <element name="TEST TEST TEST">
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60 <collection type="paired">
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61 <element name="forward" value="Input/forward_big.fastq.gz" ftype="fastqsanger.gz" />
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62 <element name="reverse" value="Input/reverse_big.fastq.gz" ftype="fastqsanger.gz" />
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63 </collection>
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64 </element>
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65 </collection>
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66 </param>
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67 <output name="output" value="Output/output.tsv" />
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68 </test>
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69 </tests>
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70 <help><![CDATA[
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71 TODO: Fill in help.
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72 ]]></help>
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73 </tool> |
