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comparison seqkit_head.xml @ 0:72dee733bcfc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
author iuc
date Sat, 08 Feb 2025 10:45:57 +0000
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-1:000000000000 0:72dee733bcfc
1 <tool id="seqkit_head" name="SeqKit Head" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Displays N records of a FASTA or FASTQ file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 #set $input_fn='input.' + str($input.ext)
10 #set $output_fn='seqkithead_output.' + str($output.ext)
11 ln -s '$input' '$input_fn'
12 && seqkit head
13 '$input_fn'
14 --number '$number'
15 -o '$output_fn'
16 --threads \${GALAXY_SLOTS:-4}
17
18 ]]></command>
19 <inputs>
20 <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
21 <param argument="--number" type="integer" value="10" label="Output first N FASTA/Q records"/>
22 </inputs>
23 <outputs>
24 <data name="output" format_source="input" from_work_dir="seqkithead_output.*" label="${input.name} Head (${tool.name})"/>
25 </outputs>
26 <tests>
27 <!-- 1. fastq.gz -->
28 <test expect_num_outputs="1">
29 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
30 <param name="number" value="10"/>
31 <output name="output" file="head_output1.fastq.gz" ftype="fastqsanger.gz"/>
32 </test>
33 <!-- 2. fasta.gz -->
34 <test expect_num_outputs="1">
35 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
36 <param name="number" value="10"/>
37 <output name="output" file="head_output2.fasta.gz" ftype="fasta.gz"/>
38 </test>
39 </tests>
40 <help>
41 **What it does**
42
43 Prints first N FASTA/Q records,
44
45 </help>
46 <expand macro="citations"/>
47 </tool>