Mercurial > repos > iuc > obi_clean

annotate obiclean.xml @ 1:1c0f0787bbcb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
author iuc
date Fri, 12 Oct 2018 06:19:41 -0400
parents 246e10039ee0
children d13f3cc6cd60
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1c0f0787bbcb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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1 <tool id="obi_clean" name="obiclean" version="@TOOL_VERSION@">
0
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2 <description>tags a set of sequences for PCR/sequencing errors identification</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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9 <command>
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11 <![CDATA[
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12 obiclean
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14 #if $distance
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15 -d '$distance'
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16 #end if
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17 #if $key
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18 -s '$key'
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19 #end if
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20 #if $ratio
246e10039ee0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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21 -r '$ratio'
246e10039ee0 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 ]]>
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30 </command>
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32 <inputs>
246e10039ee0 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" />
246e10039ee0 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)" />
246e10039ee0 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" />
246e10039ee0 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)" />
246e10039ee0 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?" />
246e10039ee0 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>
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40 <data format="fasta" name="output" label="output with ${tool.name} on ${on_string}" />
246e10039ee0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="input" value="output_obiannotate.fasta" />
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45 <param name="head" value="True"/>
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46 <output name="output" file="output_obiclean_simple.fasta" ftype="fasta"/>
246e10039ee0 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>
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49 <param name="input" value="output_obiannotate.fasta" />
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50 <param name="key" value="merged_sample"/>
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51 <param name="ratio" value="0.05"/>
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52 <param name="head" value="False"/>
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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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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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72
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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>