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comparison obitab.xml @ 5:f4b2faaa9efb draft default tip

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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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4:d5d44f7d6e4a 5:f4b2faaa9efb
1 <tool id="obi_tab" name="obitab" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="obi_tab" name="obitab" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>converts sequence file to a tabular file</description> 2 <description>converts sequence file to a tabular file</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @GUNZIP_INPUT@ 10 @GUNZIP_INPUT@
11 11
18 ${no_definition_option} 18 ${no_definition_option}
19 @INPUT_FORMAT@ 19 @INPUT_FORMAT@
20 input > '$output' 20 input > '$output'
21 ]]></command> 21 ]]></command>
22 <inputs> 22 <inputs>
23 <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" /> 23 <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file"/>
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"/> 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"/>
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"/> 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"/>
26 <param name="additional_file" type="data" optional="true" format="tabular" label="filter attributes from tabular file" /> 26 <param name="additional_file" type="data" optional="true" format="tabular" label="filter attributes from tabular file"/>
27 <expand macro="input_format_options_macro"/> 27 <expand macro="input_format_options_macro"/>
28 </inputs> 28 </inputs>
29 <outputs> 29 <outputs>
30 <data format="tabular" name="output"/> 30 <data format="tabular" name="output"/>
31 </outputs> 31 </outputs>
32 <tests> 32 <tests>
33 <test> 33 <test expect_num_outputs="1">
34 <param name="input" value="output_obisort.fastq" /> 34 <param name="input" value="output_obisort.fastq" />
35 <param name="output_seq_option" value="False"/> 35 <param name="output_seq_option" value="False"/>
36 <param name="no_definition_option" value="True"/> 36 <param name="no_definition_option" value="True"/>
37 <output name="output" file="output_obitab.txt" ftype="tabular"/> 37 <output name="output" file="output_obitab.txt" ftype="tabular"/>
38 </test> 38 </test>