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