annotate rename_scaffold.xml @ 7:9027a4b529c3 draft default tip

planemo upload commit a5a68ac1b3d4be4b923912f497ba81c6305e18f1

1 <tool id="rename_scaffold" name="rename the scaffolds" version="2.3">
2     <description>a Galaxy tool to rename or truncate the scaffold names in the target genome so that they won't exceed 31 characters</description>
3 <stdio>
4     <exit_code range="1:" />
5 </stdio>
6 <command><![CDATA[
7     python $__tool_directory__/rename.py $input $manipulate_selector $output $index
8 ]]></command>
9 <inputs>
10     <param name="input" type="data" format="fasta"/>
11     <param name="manipulate_selector" type="select" label="Choose whether you want to rename the scaffolds or truncate the scaffold names">
12         <option value="truncate" selected="true">Truncate the scaffold names if they exceed 31 characters</option>
13         <option value="rename">Rename the scaffold names</option>
14     </param>
15 </inputs>
16 <outputs>
17     <data name="output" format="fasta" label="${tool.name} on ${on_string}: ${manipulate_selector}d target genome" />
18     <data name="index" format="csv" label="${tool.name} on ${on_string}: name mapping" />
19 </outputs>
20 <tests>
21     <test>
22         <!-- Test rename input Dbia3.fa -->
23         <param name="input" value="Dbia3.fa" />
24         <param name="manipulate_selector" value="rename" />
25         <output name="output" file="Dbia3_renamed.fa"/>
26         <output name="index" file="renamed_Dbia3_name_mapping.csv"/>
27     </test>
28     <test>
29         <!-- Test truncate input Dbia3.fa -->
30         <param name="input" value="Dbia3.fa" />
31         <param name="manipulate_selector" value="truncate" />
32         <output name="output" file="Dbia3.fa"/>
33         <output name="index" file="truncated_Dbia3_name_mapping.csv"/>
34     </test>
35     <test>
36         <!-- Test rename input with non-ASCII charaters -->
37         <param name="input" value="sequence_with_noascii.fa" />
38         <param name="manipulate_selector" value="rename" />
39         <output name="output" file="renamed_sequence_with_noascii.fa" />
40         <output name="index" file="renamed_noascii_name_mapping.csv"/>
41     </test>
42     <test>
43         <!-- Test truncate input with non-ASCII charaters -->
44         <param name="input" value="sequence_with_noascii.fa" />
45         <param name="manipulate_selector" value="truncate" />
46         <output name="output" file="truncated_sequence_with_noascii.fa" />
47         <output name="index" file="truncated_noascii_name_mapping.csv"/>
48     </test>
49     <test expect_failure="true">
50         <!-- Test truncate input with non-ASCII charaters. Expect fail: name conflict! -->
51         <param name="input" value="sequence_with_noascii_name_conflict.fa" />
52         <param name="manipulate_selector" value="truncate" />
53     </test>
54     <test>
55         <!-- Test input with tab -->
56         <param name="input" value="sequence_with_tab.fa" />
57         <param name="manipulate_selector" value="truncate" />
58         <output name="output" file="fixed_reference_with_tab.fasta" />
59         <output name="index" file="truncated_noascii_with_tab_name_mapping.csv"/>
60     </test>
61 </tests>
62 <help><![CDATA[
63 This tool is to rename scaffolds in the target genome so that the sequence names are less than 31 characters. Rename all scaffolds to scaffold_1, scaffold_2, ..., scaffold_N and also output a name mapping file.
64 
65 Or truncate the scaffold names that are more than 31 characters and replace each invalid character (non-ASCII, '\\t', '\\n', '\\x0b', '\\x0c', '\\r') with '_' and also output a name mapping file.
66 ]]></help>
67 <citations>
68 </citations>
69 </tool>