Mercurial > repos > iuc > seqtk

annotate seqtk_fqchk.xml @ 8:d3b46dec1f5e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit e5a5ad091c621348dc6ce2df861475ebc54a380e
author iuc
date Tue, 13 Oct 2015 17:27:35 -0400
parents 55e75a28fde7
children 16f2535c08bf
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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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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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56 @ATTRIBUTION@
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57 ]]></help>
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55e75a28fde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 344140b8df53b8b7024618bb04594607a045c03a
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58 <expand macro="citation" />
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59 </tool>