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comparison seqkit_sort.xml @ 0:86e87375ec85 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 3dbd70c33e5adb451abd1cbd195c2e244c2b0c59
author iuc
date Mon, 27 May 2024 09:39:30 +0000
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1 <tool id="seqkit_sort" name="SeqKit sort" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>FASTA or FASTQ files</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 $output_fn='seqkitsort_output.' + str($output.ext)
11
12 ln -s '$input' '$input_fn'
13 &&
14 seqkit sort
15 '$input_fn'
16 $reverse
17 $sort_by
18 -o '$output_fn'
19 --threads \${GALAXY_SLOTS:-4}
20
21 ]]></command>
22 <inputs>
23 <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
24 <param name="sort_by" type="select" label="Sort by:">
25 <option value="" selected="true">Sequence ID</option>
26 <option value="--by-bases">Non-gap bases</option>
27 <option value="--by-length">Sequence length</option>
28 <option value="--by-name">Full name (instead of just ID)</option>
29 <option value="--by-seq">Sequence</option>
30 </param>
31 <param argument="--reverse" type="boolean" truevalue="--reverse" falsevalue="" checked="false" label="Reverse the result?"/>
32 </inputs>
33 <outputs>
34 <data name="output" format_source="input" from_work_dir="seqkitsort_output.*" label="${input.name} sorted (${tool.name})"/>
35 </outputs>
36 <tests>
37 <!-- 1. fastq.gz -->
38 <test expect_num_outputs="1">
39 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
40 <output name="output" file="sort_output1.fastq.gz" ftype="fastqsanger.gz"/>
41 </test>
42 <!-- 2. fasta.gz -->
43 <test expect_num_outputs="1">
44 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
45 <output name="output" file="sort_output2.fasta.gz" ftype="fasta.gz"/>
46 </test>
47 <!-- 3. by-bases, forward, fasta -->
48 <test expect_num_outputs="1">
49 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
50 <param name="sort_by" value="--by-bases"/>
51 <output name="output" file="sort_output3.fasta.gz" ftype="fasta.gz"/>
52 </test>
53 <!-- 4. by-length, rev, fasta -->
54 <test expect_num_outputs="1">
55 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
56 <param name="reverse" value="true"/>
57 <param name="sort_by" value="--by-length"/>
58 <output name="output" file="sort_output4.fasta.gz" ftype="fasta.gz"/>
59 </test>
60 <!-- 5. by-name, forward, fastq -->
61 <test expect_num_outputs="1">
62 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
63 <param name="sort_by" value="--by-name"/>
64 <output name="output" file="sort_output5.fastq.gz" ftype="fastqsanger.gz"/>
65 </test>
66 <!-- 6. by-seq, rev, fastq -->
67 <test expect_num_outputs="1">
68 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
69 <param name="reverse" value="true"/>
70 <param name="sort_by" value="--by-seq"/>
71 <output name="output" file="sort_output6.fastq.gz" ftype="fastqsanger.gz"/>
72 </test>
73 </tests>
74 <help>
75 **What it does**
76
77 Sort sequences (FASTA, FASTQ) by id, name, sequence, or length.
78
79 </help>
80 <expand macro="citations"/>
81 </tool>