Mercurial > repos > iuc > obi_clean

annotate obiclean.xml @ 0:f4e449660000 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
author iuc
date Wed, 12 Apr 2017 17:39:09 -0400
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children 1405e4efffed
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f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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1 <tool id="obi_clean" name="obiclean" version="@WRAPPER_VERSION@">
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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2 <description>tags a set of sequences for PCR/sequencing errors identification</description>
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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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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9 <command>
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f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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11 <![CDATA[
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12 obiclean
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14 #if $distance
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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15 -d '$distance'
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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16 #end if
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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17 #if $key
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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18 -s '$key'
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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19 #end if
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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20 #if $ratio
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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21 -r '$ratio'
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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22 #end if
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23 ${head}
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25 '$input'>'$output'
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28 ]]>
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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30 </command>
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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32 <inputs>
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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33 <param name="input" type="data" format="fasta" label="Input sequences file" />
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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34 <param name="distance" type="integer" value="1" optional="true" label="Maximum numbers of differences between two variant sequences (default: 1)" />
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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35 <param name="key" type="text" optional="true" label="Specify an attribute containing sample definition" />
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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36 <param name="ratio" optional="true" type="float" value="1" label="Threshold ratio between counts (rare/abundant counts) of two sequence records so that the less abundant one is a variant of the more abundant (default: 1, i.e. all less abundant sequences are variants)" />
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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37 <param name="head" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Do you want to select only sequences with the head status in a least one sample?" />
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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38 </inputs>
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39 <outputs>
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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40 <data format="fasta" name="output" label="output with ${tool.name} on ${on_string}" />
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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41 </outputs>
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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42 <tests>
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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43 <test>
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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44 <param name="input" value="output_obiannotate.fasta" />
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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45 <param name="head" value="True"/>
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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46 <output name="output" file="output_obiclean_simple.fasta" ftype="fasta"/>
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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47 </test>
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48 <test>
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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49 <param name="input" value="output_obiannotate.fasta" />
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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50 <param name="key" value="merged_sample"/>
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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51 <param name="ratio" value="0.05"/>
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52 <param name="head" value="False"/>
f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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53 <output name="output" file="output_obiclean_advanced.fasta" ftype="fasta"/>
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54 </test>
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55 </tests>
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56 <help><![CDATA[
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57
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58 .. class:: infomark
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f4e449660000 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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60 **What it does**
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62 obijoinpairedend aims at joining the two reads of a paired-end library.
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64 For this purpose, it concatenates sequence merging the forward read and the reversed-complemented reverse read.
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65
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66 The program uses as input one or two sequences reads files.
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67
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68 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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69 If just one file is provided, sequence records are supposed to be all of the same length. The first half of the sequence is used as forward read, the second half is used as the reverse read.
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70
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71 @OBITOOLS_LINK@
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73 ]]>
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74 </help>
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75 <expand macro="citation" />
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76 </tool>