Mercurial > repos > greg > pyfaidx

comparison pyfaidx.xml @ 0:fb6a4e2d6234 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Tue, 10 Oct 2023 13:23:15 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:fb6a4e2d6234
1 <tool id="pyfaidx" name="pyfaidx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>efficient FASTA indexing</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 #if $input.is_of_type('fasta.gz'):
9 gunzip -c '$input' > 'input.fasta' &&
10 #else:
11 ln -s '$input' 'input.fasta' &&
12 #end if
13 faidx -i chromsizes 'input.fasta' > '$output'
14 ]]></command>
15 <inputs>
16 <param name="input" type="data" format="fasta,fasta.gz" label="Assembled FASTA file"/>
17 </inputs>
18 <outputs>
19 <data name="output" format="fasta"/>
20 </outputs>
21 <tests>
22 <test>
23 <param name="input" value="input.fasta.gz" ftype="fasta.gz"/>
24 <output name="output" ftype="fasta">
25 <assert_contents>
26 <has_size value="51690"/>
27 <has_text text=">contig_10"/>
28 <has_text text=">contig_7"/>
29 </assert_contents>
30 </output>
31 </test>
32 </tests>
33 <help>
34 **What it does**
35
36 Runs faidx to index the input FASTA file.
37 </help>
38 <expand macro="citations"/>
39 </tool>
40