Mercurial > repos > iuc > seqtk
annotate seqtk_trimfq.xml @ 2:f73729b62b51 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2249d643284ee782d882cd200729a86a2c6bb744
| author | iuc |
|---|---|
| date | Fri, 01 Jan 2016 14:49:42 -0500 |
| parents | e0a0fd938de4 |
| children | bc7d99f46a5d |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool id="seqtk_trimfq" name="seqtk_trimfq" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>trim FASTQ using the Phred algorithm</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <expand macro="stdio"/> | |
| 9 <command><![CDATA[seqtk trimfq | |
| 10 #if $mode.mode_select == "quality": | |
| 11 -q $mode.q | |
| 12 -l $mode.l | |
| 13 #else: | |
| 14 -b $mode.b | |
| 15 -e $mode.e | |
| 16 #end if | |
| 17 $in_file | |
| 18 > $default]]></command> | |
| 19 <inputs> | |
| 20 <expand macro="in_faq"/> | |
| 21 <conditional name="mode"> | |
| 22 <param name="mode_select" type="select" label="Mode for trimming FASTQ File"> | |
| 23 <option value="quality">Quality</option> | |
| 24 <option value="position">Length/Position</option> | |
| 25 </param> | |
| 26 <when value="quality"> | |
| 27 <param label="error rate threshold" help="(-q)" name="q" type="float" value="0.05"/> | |
| 28 <param label="maximally trim down to INT bp" help="(-l)" name="l" type="integer" value="30"/> | |
| 29 </when> | |
| 30 <when value="position"> | |
| 31 <param label="trim INT bp from left" help="(-b)" name="b" type="integer" value="0"/> | |
| 32 <param label="trim INT bp from right" help="(-e)" name="e" type="integer" value="0"/> | |
| 33 </when> | |
| 34 </conditional> | |
| 35 </inputs> | |
| 36 <outputs> | |
| 37 <data format_source="in_file" hidden="false" name="default" label="$in_file.name trimmed"/> | |
| 38 </outputs> | |
| 39 <tests> | |
| 40 <test> | |
| 41 <param name="in_file" value="seqtk_trimfq.fq"/> | |
| 42 <param name="mode_select" value="quality"/> | |
| 43 <param name="q" value="0.05"/> | |
| 44 <param name="l" value="30"/> | |
| 45 <output name="default" file="seqtk_trimfq_default.fq" ftype="fastq"/> | |
| 46 </test> | |
| 47 <test> | |
| 48 <param name="in_file" value="seqtk_trimfq.fq"/> | |
| 49 <param name="mode_select" value="position"/> | |
| 50 <param name="b" value="5"/> | |
| 51 <param name="e" value="5"/> | |
| 52 <output name="default" file="seqtk_trimfq_be.fq" ftype="fastq"/> | |
| 53 </test> | |
| 54 </tests> | |
| 55 <help><![CDATA[ | |
| 56 **What it does** | |
| 57 | |
| 58 Trim a fastq file based on Phred scores, or by length | |
| 59 | |
| 60 @ATTRIBUTION@ | |
| 61 ]]></help> | |
|
2
f73729b62b51
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2249d643284ee782d882cd200729a86a2c6bb744
iuc
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|
62 <expand macro="citation" /> |
| 0 | 63 </tool> |