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1 <?xml version="1.0"?>
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2 <tool id="seqtk_fqchk" name="seqtk_fqchk" version="@WRAPPER_VERSION@.0">
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3 <description>fastq QC (base/quality summary)</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[seqtk fqchk
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10 -q $q
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11 $in_file | awk '{if(NR<4){print "#"$0}else{print $0}}'
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12 > $default]]></command>
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13 <inputs>
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14 <expand macro="in_fq"/>
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15 <param name="q" type="integer" value="20" label="quality values" help="use 0 to get the distribution of all quality values (-q)"/>
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16 </inputs>
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17 <outputs>
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18 <data format="tabular" hidden="false" name="default" label="Quality information for $in_file.name"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="in_file" value="seqtk_fqchk.fq"/>
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23 <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
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24 </test>
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25 </tests>
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26 <help><![CDATA[
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27 **What it does**
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28
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29 Returns quality score information base-by-base.
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30
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31 ::
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32
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33 @SEQ_ID1
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34 GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
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35 +
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36 !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
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37
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38 each based is examined individually and information reported:
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39
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40 ::
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41
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42 #min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values
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43 #POS #bases %A %C %G %T %N avgQ errQ %low %high
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44 #ALL 60 31.7 16.7 18.3 33.3 0.0 15.1 8.7 66.7 33.3
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45 1 1 0.0 0.0 100.0 0.0 0.0 0.0 3.0 100.0 0.0
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46 2 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0
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47 3 1 0.0 0.0 0.0 100.0 0.0 6.0 6.0 100.0 0.0
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48 4 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
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49 5 1 0.0 0.0 0.0 100.0 0.0 7.0 7.0 100.0 0.0
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50 6 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
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51 7 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
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52 8 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
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53 9 1 0.0 0.0 100.0 0.0 0.0 9.0 9.0 100.0 0.0
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54 10 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
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55
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56 @ATTRIBUTION@
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57 ]]></help>
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58 </tool>
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