Mercurial > repos > portiahollyoak > change_fasta_header_using_tabular_file

comparison change_fasta_header_using_tabular_file.xml @ 0:540425dc9746 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
author portiahollyoak
date Fri, 22 Apr 2016 12:07:53 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:540425dc9746
1 <tool id ="change_fasta_header_using_tabular_file" name="Change fasta header" version=" 0.1.0">
2 <description>using a tabular file</description>
3 <stdio>
4 <exit_code range="1:" />
5 </stdio>
6 <command>python $__tool_directory__/change_fasta_header_using_tabular_file.py
7 --tab_input "$input1"
8 --fasta_input "$input2"
9 "$output"
10 </command>
11 <inputs>
12 <param format="tabular" name="input1" type="data" label="Tabular File"/>
13 <param format="fasta" name="input2" type="data" label="Fasta file"/>
14 </inputs>
15 <outputs>
16 <data format="fasta" name="output" />
17 </outputs>
18 <tests>
19 <test>
20 <param name="input1" value="tabular_file.tsv" ftype="tabular"/>
21 <param name="input2" value="genbank_input.fasta" ftype="fasta"/>
22 <output name="output" file="output.fasta"/>
23 </test>
24 </tests>
25 <help> <![CDATA[
26
27 This tool takes 2 input files, a tabular file with text to replace in the first column,
28 and a replacement text in the 2nd column, as well as a fasta file.
29 Every occurence of values in the first column of the tabular file will be replaced with the
30 value in the 2nd column.
31
32 -----
33
34 *Example*
35
36 **Fasta header** ::
37
38 >RT1C
39 ATGCATGC
40
41 **Tabular file** ::
42
43 RT1C Rt1c
44
45 **Output file** ::
46
47 >Rt1c
48 ATGCATGC
49
50
51 ]]> </help>
52 </tool>