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comparison fasta_concatenate_by_species.xml @ 2:16df616b39e5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
author devteam
date Sun, 01 Mar 2020 07:24:26 -0500
parents 717aee069681
children
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1:717aee069681 2:16df616b39e5
1 <tool id="fasta_concatenate0" name="Concatenate" version="0.0.0"> 1 <tool id="fasta_concatenate0" name="Concatenate" version="0.0.1" profile="16.04">
2 <description>FASTA alignment by species</description> 2 <description>FASTA alignment by species</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.7.1">bx-python</requirement> 4 <requirement type="package" version="0.8.8">bx-python</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python">fasta_concatenate_by_species.py $input1 $out_file1</command> 6 <command>
7 python '$__tool_directory__/fasta_concatenate_by_species.py'
8 '$input1'
9 '$out_file1'
10 </command>
7 <inputs> 11 <inputs>
8 <param name="input1" type="data" format="fasta" label="FASTA alignment"/> 12 <param name="input1" type="data" format="fasta" label="FASTA alignment"/>
9 </inputs> 13 </inputs>
10 <outputs> 14 <outputs>
11 <data name="out_file1" format="fasta"/> 15 <data name="out_file1" format="fasta"/>
14 <test> 18 <test>
15 <param name="input1" value="cf_maf2fasta.dat" /> 19 <param name="input1" value="cf_maf2fasta.dat" />
16 <output name="out_file1" file="fasta_concatenate_out.fasta" /> 20 <output name="out_file1" file="fasta_concatenate_out.fasta" />
17 </test> 21 </test>
18 </tests> 22 </tests>
19 <help> 23 <help><![CDATA[
20 24
21 **What it does** 25 **What it does**
22 26
23 This tools attempts to parse FASTA headers to determine the species for each sequence in a multiple FASTA alignment. 27 This tools attempts to parse FASTA headers to determine the species for each sequence in a multiple FASTA alignment.
24 It then linearly concatenates the sequences for each species in the file, creating one sequence per determined species. 28 It then linearly concatenates the sequences for each species in the file, creating one sequence per determined species.
69 73
70 .. class:: warningmark 74 .. class:: warningmark
71 75
72 This tool will only work properly on files with Galaxy style FASTA headers. 76 This tool will only work properly on files with Galaxy style FASTA headers.
73 77
74 </help> 78 ]]></help>
75 </tool> 79 </tool>