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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
author iuc
date Thu, 30 Oct 2025 16:01:54 +0000
parents d5d44f7d6e4a
children
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d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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1 <tool id="obi_tab" name="obitab" version="@TOOL_VERSION@" profile="@PROFILE@">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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2 <description>converts sequence file to a tabular file</description>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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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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f4b2faaa9efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
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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 <command><![CDATA[
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10 @GUNZIP_INPUT@
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12 obitab
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13 --without-progress-bar
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14 #if $additional_file
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15 --omit-attribute='$additional_file'
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16 #end if
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17 ${output_seq_option}
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18 ${no_definition_option}
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19 @INPUT_FORMAT@
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20 input > '$output'
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21 ]]></command>
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22 <inputs>
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23 <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file"/>
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24 <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"/>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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25 <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"/>
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26 <param name="additional_file" type="data" optional="true" format="tabular" label="filter attributes from tabular file"/>
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27 <expand macro="input_format_options_macro"/>
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28 </inputs>
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29 <outputs>
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30 <data format="tabular" name="output"/>
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31 </outputs>
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32 <tests>
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33 <test expect_num_outputs="1">
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34 <param name="input" value="output_obisort.fastq" />
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35 <param name="output_seq_option" value="False"/>
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36 <param name="no_definition_option" value="True"/>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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37 <output name="output" file="output_obitab.txt" ftype="tabular"/>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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43 .. class:: infomark
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45 **What it does**
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47 obitab command converts sequence file to a tabular file that can be open by a spreadsheet program or R
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49 @OBITOOLS_LINK@
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50
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51 ]]>
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52 </help>
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53 <expand macro="citation" />
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54 </tool>