Mercurial > repos > greg > pyfaidx
comparison pyfaidx.xml @ 0:fb6a4e2d6234 draft default tip
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author | greg |
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date | Tue, 10 Oct 2023 13:23:15 +0000 |
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-1:000000000000 | 0:fb6a4e2d6234 |
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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 |