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comparison seqtk_trimfq.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
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2:f73729b62b51 3:bc7d99f46a5d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="seqtk_trimfq" name="seqtk_trimfq" version="@WRAPPER_VERSION@.0"> 2 <tool id="seqtk_trimfq" name="seqtk_trimfq" version="@WRAPPER_VERSION@.0">
3 <description>trim FASTQ using the Phred algorithm</description> 3 <description>trim FASTQ using the Phred algorithm</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 trimfq 9 <command><![CDATA[
10 seqtk trimfq
10 #if $mode.mode_select == "quality": 11 #if $mode.mode_select == "quality":
11 -q $mode.q 12 -q $mode.q
12 -l $mode.l 13 -l $mode.l
13 #else: 14 #else:
14 -b $mode.b 15 -b $mode.b
15 -e $mode.e 16 -e $mode.e
16 #end if 17 #end if
17 $in_file 18 '$in_file'
18 > $default]]></command> 19 > '$default'
19 <inputs> 20 ]]></command>
20 <expand macro="in_faq"/> 21 <inputs>
21 <conditional name="mode"> 22 <expand macro="in_faq"/>
22 <param name="mode_select" type="select" label="Mode for trimming FASTQ File"> 23 <conditional name="mode">
23 <option value="quality">Quality</option> 24 <param name="mode_select" type="select" label="Mode for trimming FASTQ File">
24 <option value="position">Length/Position</option> 25 <option value="quality">Quality</option>
25 </param> 26 <option value="position">Length/Position</option>
26 <when value="quality"> 27 </param>
27 <param label="error rate threshold" help="(-q)" name="q" type="float" value="0.05"/> 28 <when value="quality">
28 <param label="maximally trim down to INT bp" help="(-l)" name="l" type="integer" value="30"/> 29 <param argument="-q" type="float" value="0.05" label="Error rate threshold" />
29 </when> 30 <param argument="-l" type="integer" value="30" label="Maximally trim down to INT bp" />
30 <when value="position"> 31 </when>
31 <param label="trim INT bp from left" help="(-b)" name="b" type="integer" value="0"/> 32 <when value="position">
32 <param label="trim INT bp from right" help="(-e)" name="e" type="integer" value="0"/> 33 <param argument="-b" type="integer" value="0" label="Trim INT bp from left" />
33 </when> 34 <param argument="-e" type="integer" value="0" label="Trim INT bp from right" />
34 </conditional> 35 </when>
35 </inputs> 36 </conditional>
36 <outputs> 37 </inputs>
37 <data format_source="in_file" hidden="false" name="default" label="$in_file.name trimmed"/> 38 <outputs>
38 </outputs> 39 <data name="default" format_source="in_file" label="$in_file.name trimmed"/>
39 <tests> 40 </outputs>
40 <test> 41 <tests>
41 <param name="in_file" value="seqtk_trimfq.fq"/> 42 <test>
42 <param name="mode_select" value="quality"/> 43 <param name="in_file" value="seqtk_trimfq.fq"/>
43 <param name="q" value="0.05"/> 44 <param name="mode_select" value="quality"/>
44 <param name="l" value="30"/> 45 <param name="q" value="0.05"/>
45 <output name="default" file="seqtk_trimfq_default.fq" ftype="fastq"/> 46 <param name="l" value="30"/>
46 </test> 47 <output name="default" file="seqtk_trimfq_default.fq" ftype="fastq"/>
47 <test> 48 </test>
48 <param name="in_file" value="seqtk_trimfq.fq"/> 49 <test>
49 <param name="mode_select" value="position"/> 50 <param name="in_file" value="seqtk_trimfq.fq"/>
50 <param name="b" value="5"/> 51 <param name="mode_select" value="position"/>
51 <param name="e" value="5"/> 52 <param name="b" value="5"/>
52 <output name="default" file="seqtk_trimfq_be.fq" ftype="fastq"/> 53 <param name="e" value="5"/>
53 </test> 54 <output name="default" file="seqtk_trimfq_be.fq" ftype="fastq"/>
54 </tests> 55 </test>
55 <help><![CDATA[ 56 </tests>
57 <help><![CDATA[
56 **What it does** 58 **What it does**
57 59
58 Trim a fastq file based on Phred scores, or by length 60 Trim a fastq file based on Phred scores, or by length
59 61
60 @ATTRIBUTION@ 62 @ATTRIBUTION@
61 ]]></help> 63 ]]></help>
62 <expand macro="citation" /> 64 <expand macro="citation" />
63 </tool> 65 </tool>