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annotate obitab.xml @ 1:c92e057db87a 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 06:26:39 -0400
parents e606e311396a
children 5f7003111e32
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c92e057db87a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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1 <tool id="obi_tab" name="obitab" version="@TOOL_VERSION@">
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2 <description>converts sequence file to a tabular file that can be open by a spreadsheet program or R</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"/>
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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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 obitab
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13 #if $additional_file
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14 --omit-attribute='$additional_file'
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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15 #end if
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16 ${output_seq_option}
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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17 ${no_definition_option}
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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18 ${options_inputtype}
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19 ${options_seqtype}
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21 '$input' > '$output'
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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22 ]]>
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24 </command>
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26 <inputs>
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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27 <param name="input" type="data" format="fastq,fasta,txt,tabular" label="Input sequences file" />
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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28 <param name="output_seq_option" type="boolean" checked="false" truevalue="-o" falsevalue="" label="Do you want to add an extra column?" help="Use this option if you want to add an extra column at the end of the table for the sequence itself"/>
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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29 <param name="no_definition_option" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Do you want to remove column containing the sequence definition?" help="Use this option if you want to remove column containing the sequence definition in the output tab file"/>
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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30 <param name="additional_file" type="data" optional="true" format="tabular" label="filter attributes from tabular file" />
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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31 <param name="options_inputtype" type="select" label="Specify the input datatype">
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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32 <expand macro="inputtype"/>
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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33 </param>
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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34 <param name="options_seqtype" type="select" label="Specify the sequence datatype" >
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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35 <option value="--nuc" selected="true">nucleic</option>
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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36 <option value="--prot">protein</option>
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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37 </param>
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38 </inputs>
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39 <outputs>
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40 <data format="tabular" name="output" label="output.tabular with ${tool.name} on ${on_string}" />
e606e311396a 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_obisort.fastq" />
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45 <param name="output_seq_option" value="False"/>
e606e311396a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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46 <param name="no_definition_option" value="True"/>
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47 <param name="options_inputtype" value="fasta"/>
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48 <param name="options_seqtype" value="--prot"/>
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49 <output name="output" file="output_obitab.txt" ftype="tabular"/>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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55 .. class:: infomark
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57 **What it does**
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59 obitab command converts sequence file to a tabular file that can be open by a spreadsheet program or R
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61 @OBITOOLS_LINK@
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63 ]]>
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64 </help>
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65 <expand macro="citation" />
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66 </tool>