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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta commit 01140c0ac1a926856c55853a0028e5d44935d9e6"
author devteam
date Wed, 05 Feb 2020 10:51:52 -0500
parents 0b4e36026794
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0:0b4e36026794 1:0a7799698fe5
1 <tool id="tab2fasta" name="Tabular-to-FASTA" version="1.1.0"> 1 <tool id="tab2fasta" name="Tabular-to-FASTA" version="1.1.1" profile="16.04">
2 <description>converts tabular file to FASTA format</description> 2 <description>converts tabular file to FASTA format</description>
3 <command interpreter="python">tabular_to_fasta.py $input $title_col $seq_col $output </command> 3 <requirements>
4 <inputs> 4 <requirement type="package" version="3.7">python</requirement>
5 <param name="input" type="data" format="tabular" label="Tab-delimited file"/> 5 </requirements>
6 <param name="title_col" type="data_column" data_ref="input" multiple="True" numerical="False" label="Title column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"/> 6 <command><![CDATA[
7 <param name="seq_col" type="data_column" data_ref="input" numerical="False" label="Sequence column" /> 7 python '$__tool_directory__/tabular_to_fasta.py'
8 </inputs> 8 '$input'
9 <outputs> 9 $title_col
10 <data name="output" format="fasta"/> 10 $seq_col
11 </outputs> 11 '$output'
12 <tests> 12 ]]></command>
13 <test> 13 <inputs>
14 <param name="input" value="solexa.tabular" /> 14 <param name="input" type="data" format="tabular" label="Tab-delimited file"/>
15 <param name="title_col" value="1,2,3,4" /> 15 <param name="title_col" type="data_column" data_ref="input" multiple="true" numerical="false" label="Title column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"/>
16 <param name="seq_col" value="5" /> 16 <param name="seq_col" type="data_column" data_ref="input" numerical="false" label="Sequence column" />
17 <output name="output" file="tabular_to_fasta_out1.fasta" /> 17 </inputs>
18 </test> 18 <outputs>
19 </tests> 19 <data name="output" format="fasta"/>
20 <help> 20 </outputs>
21 21 <tests>
22 <test>
23 <param name="input" value="solexa.tabular" />
24 <param name="title_col" value="1,2,3,4" />
25 <param name="seq_col" value="5" />
26 <output name="output" file="tabular_to_fasta_out1.fasta" />
27 </test>
28 </tests>
29 <help><![CDATA[
22 **What it does** 30 **What it does**
23 31
24 Converts tab delimited data into FASTA formatted sequences. 32 Converts tab delimited data into FASTA formatted sequences.
25 33
26 ----------- 34 -----------
27 35
28 **Example** 36 **Example**
29 37
30 Suppose this is a sequence file produced by Illumina (Solexa) sequencer:: 38 Suppose this is a sequence file produced by Illumina (Solexa) sequencer::
31 39
32 5 300 902 419 GACTCATGATTTCTTACCTATTAGTGGTTGAACATC 40 5 300 902 419 GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
33 5 300 880 431 GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT 41 5 300 880 431 GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
34 42
35 Selecting **c3** and **c4** as the **Title column(s)** and **c5** as the **Sequence column** will result in:: 43 Selecting **c3** and **c4** as the **Title column(s)** and **c5** as the **Sequence column** will result in::
36 44
37 &gt;902_419 45 >902_419
38 GACTCATGATTTCTTACCTATTAGTGGTTGAACATC 46 GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
39 &gt;880_431 47 >880_431
40 GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT 48 GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
41 49 ]]></help>
42 </help>
43 </tool> 50 </tool>