Mercurial > repos > iuc > obi_clean

annotate obiclean.xml @ 4:08d873cdd5f6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author iuc
date Wed, 20 Mar 2024 13:17:36 +0000
parents 12baadec7809
children
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4
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
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1 <tool id="obi_clean" name="obiclean" version="@TOOL_VERSION@" profile="@PROFILE@">
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iuc
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2 <description>tags a set of sequences for PCR/sequencing errors identification</description>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
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3 <macros>
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iuc
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4 <import>macros.xml</import>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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5 </macros>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9
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10 <command><![CDATA[
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11 @GUNZIP_INPUT@
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12 obiclean
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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13 --without-progress-bar
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14 #if $distance
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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15 -d '$distance'
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16 #end if
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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17 #if $key
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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18 -s '$key'
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19 #end if
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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20 #if $ratio
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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21 -r '$ratio'
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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22 #end if
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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23 ${head}
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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24 @INPUT_FORMAT@
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25 @OUT_FORMAT@
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26 input
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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27 @GZIP_OUTPUT@
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28 >'$output'
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29 @GENERATE_GALAXY_JSON@
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30 ]]></command>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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31 <inputs>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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32 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file"/>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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33 <param name="distance" type="integer" value="1" optional="true" label="Maximum numbers of differences between two variant sequences (default: 1)"/>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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34 <param name="key" type="text" optional="true" label="Specify an attribute containing sample definition"/>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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35 <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)"/>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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36 <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?"/>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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37 <expand macro="input_format_options_macro"/>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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38 <expand macro="out_format_macro"/>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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39 </inputs>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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40 <outputs>
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41 <data format="auto" name="output"/>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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42 </outputs>
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43 <tests>
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44 <test expect_num_outputs="1">
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45 <param name="input" value="output_obiannotate.fasta" />
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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46 <param name="head" value="True"/>
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47 <output name="output" file="output_obiclean_simple.fasta" ftype="fasta"/>
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48 </test>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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49 <test expect_num_outputs="1">
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50 <param name="input" value="output_obiannotate.fasta.gz" />
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51 <param name="key" value="merged_sample"/>
08d873cdd5f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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52 <param name="ratio" value="0.05"/>
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53 <param name="head" value="False"/>
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54 <output name="output" file="output_obiclean_advanced.fasta.gz" ftype="fasta.gz" decompress="true"/>
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58
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59 .. class:: infomark
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60
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61 **What it does**
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62
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63 obijoinpairedend aims at joining the two reads of a paired-end library.
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64
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65 For this purpose, it concatenates sequence merging the forward read and the reversed-complemented reverse read.
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66
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67 The program uses as input one or two sequences reads files.
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68
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69 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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70 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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71
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72 @OBITOOLS_LINK@
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73
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74 ]]>
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75 </help>
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76 <expand macro="citation"/>
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77 </tool>