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annotate seqtk_fqchk.xml @ 5:a09586d5149a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
author iuc
date Fri, 11 Jan 2019 05:15:20 -0500
parents ecf1c30da3a2
children 3da72230c066
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_fqchk" name="seqtk_fqchk" version="@TOOL_VERSION@.1">
3
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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 <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
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9 </expand>
3
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10 <expand macro="stdio"/>
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11 <command><![CDATA[
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12 seqtk fqchk
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13 -q $q
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14 '$in_file' | awk '{if(NR<4){print "#"$0}else{print $0}}'
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15 > '$default'
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16 ]]></command>
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17 <inputs>
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18 <expand macro="in_fq"/>
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19 <param argument="-q" type="integer" value="20" label="Quality values" help="Use 0 to get the distribution of all quality values"/>
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20 </inputs>
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21 <outputs>
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22 <data name="default" format="tabular" label="Quality information for $in_file.name"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="in_file" value="seqtk_fqchk.fq" ftype="fastq"/>
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27 <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
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28 </test>
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29 <test>
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30 <param name="in_file" value="seqtk_fqchk.fq.gz" ftype="fastq.gz"/>
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31 <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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35 **What it does**
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36
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37 Returns quality score information base-by-base.
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38
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39 ::
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40
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41 @SEQ_ID1
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42 GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
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43 +
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44 !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
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45
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46 each based is examined individually and information reported:
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47
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48 ::
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49
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50 #min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values
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51 #POS #bases %A %C %G %T %N avgQ errQ %low %high
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52 #ALL 60 31.7 16.7 18.3 33.3 0.0 15.1 8.7 66.7 33.3
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53 1 1 0.0 0.0 100.0 0.0 0.0 0.0 3.0 100.0 0.0
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54 2 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0
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62 10 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
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63
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64 @ATTRIBUTION@
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65 ]]></help>
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66 <expand macro="citation" />
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67 </tool>