Mercurial > repos > iuc > obi_illumina_pairend

annotate illuminapairedend.xml @ 1:0c9296704212 draft

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author iuc
date Fri, 12 Oct 2018 06:24:17 -0400
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0c9296704212 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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1 <tool id="obi_illumina_pairend" name="Illuminapairedend - Assembling pair-end reads" version="@TOOL_VERSION@">
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2 <description>Construct consensus reads from Illumina pair-end reads</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <command>
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10 <![CDATA[
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11 illuminapairedend
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13 --score-min='$score'
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14 -r '$inputfastq3p'
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15 '$inputfastq5p' > '$output'
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17 ]]>
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19 </command>
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21 <inputs>
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22 <param name="inputfastq3p" type="data" format="fastq" label="Read from file" help="file of 3p (1:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />
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23 <param name="inputfastq5p" type="data" format="fastq" label="Read from file" help="file of 5p (2:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />
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24 <param name="score" type="float" value="40.0" label="minimum score for keeping aligment"/>
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25 </inputs>
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26 <outputs>
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27 <data format="fastq" name="output" label="${tool.name} on ${on_string}: assembly results" />
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28 </outputs>
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30 <tests>
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31 <test>
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32 <param name="inputfastq3p" value="wolf_small.F.fastq" />
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33 <param name="inputfastq5p" value="wolf_small.R.fastq" />
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34 <param name="score" value="40.0" />
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35 <output name="output" file="illuminapairedend.output.fastq" ftype="fastq"/>
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36 </test>
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37 </tests>
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39 <help><![CDATA[
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41 .. class:: warning
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43 **Warning:**
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44 Sequence records corresponding to the same read pair must be in the same order in the two files
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46 --------
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48 .. class:: infomark
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50 **What it does**
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52 illuminapairedend aims at aligning the two reads of a pair-end library sequenced using an Illumina platform :
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54 \* If the two reads overlap, it returns the consensus sequence together with its quality
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55 \* Otherwise, it concatenates sequence merging the forward read and the reversed-complemented reverse read.
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57 The program uses as input one or two fastq sequences reads files.
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59 \* If two files are used one of them must be specified using the -r option. Sequence records corresponding to the same read pair must be in the same order in the two files.
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60 \* If just one file is provided, sequence records are supposed to be all of the same length. The first half of th e sequence is used as forward read, the second half is used as the reverse read.
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62 illuminapairedend align the forward sequence record with the reverse complement of the reverse sequence record. The alignment algorithm takes into account the base qualities.
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64 @OBITOOLS_LINK@
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66 ]]>
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67 </help>
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68 <expand macro="citation" />
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70 </tool>