Mercurial > repos > iuc > seqtk

comparison seqtk_fqchk.xml @ 3:bc7d99f46a5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author iuc
date Mon, 05 Jun 2017 13:27:11 -0400
parents f73729b62b51
children ecf1c30da3a2
comparison
equal deleted inserted replaced
2:f73729b62b51 3:bc7d99f46a5d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="seqtk_fqchk" name="seqtk_fqchk" version="@WRAPPER_VERSION@.0"> 2 <tool id="seqtk_fqchk" name="seqtk_fqchk" version="@WRAPPER_VERSION@.0">
3 <description>fastq QC (base/quality summary)</description> 3 <description>fastq QC (base/quality summary)</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[seqtk fqchk 9 <command><![CDATA[
10 seqtk fqchk
10 -q $q 11 -q $q
11 $in_file | awk '{if(NR<4){print "#"$0}else{print $0}}' 12 '$in_file' | awk '{if(NR<4){print "#"$0}else{print $0}}'
12 > $default]]></command> 13 > '$default'
13 <inputs> 14 ]]></command>
14 <expand macro="in_fq"/> 15 <inputs>
15 <param name="q" type="integer" value="20" label="quality values" help="use 0 to get the distribution of all quality values (-q)"/> 16 <expand macro="in_fq"/>
16 </inputs> 17 <param argument="-q" type="integer" value="20" label="Quality values" help="Use 0 to get the distribution of all quality values"/>
17 <outputs> 18 </inputs>
18 <data format="tabular" hidden="false" name="default" label="Quality information for $in_file.name"/> 19 <outputs>
19 </outputs> 20 <data name="default" format="tabular" label="Quality information for $in_file.name"/>
20 <tests> 21 </outputs>
21 <test> 22 <tests>
22 <param name="in_file" value="seqtk_fqchk.fq"/> 23 <test>
23 <output name="default" file="seqtk_fqchk.out" ftype="tabular"/> 24 <param name="in_file" value="seqtk_fqchk.fq"/>
24 </test> 25 <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
25 </tests> 26 </test>
26 <help><![CDATA[ 27 </tests>
28 <help><![CDATA[
27 **What it does** 29 **What it does**
28 30
29 Returns quality score information base-by-base. 31 Returns quality score information base-by-base.
30 32
31 :: 33 ::
52 8 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0 54 8 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
53 9 1 0.0 0.0 100.0 0.0 0.0 9.0 9.0 100.0 0.0 55 9 1 0.0 0.0 100.0 0.0 0.0 9.0 9.0 100.0 0.0
54 10 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0 56 10 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
55 57
56 @ATTRIBUTION@ 58 @ATTRIBUTION@
57 ]]></help> 59 ]]></help>
58 <expand macro="citation" /> 60 <expand macro="citation" />
59 </tool> 61 </tool>