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comparison kat_sect.xml @ 0:699eef7398c1 draft

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author nml
date Mon, 06 Feb 2017 12:36:09 -0500
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1 <tool id="kat_sect" name="KAT Sect" version="1.3.0">
2 <description> SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.</description>
3 <requirements>
4 <requirement type="package" version="2.3.1">kat</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command><![CDATA[
10
11 ln "$db" db.fasta &&
12 #if $single_or_paired.type == "single"
13 ln "$input_se" "$single_or_paired.input_se.element_identifier".fastq &&
14 kat sect 'db.fasta'
15 "$single_or_paired.input_se.element_identifier".fastq
16 #elif $single_or_paired.type == "paired"
17 ln "$single_or_paired.forward_pe" "$single_or_paired.forward_pe.name"_1.fastq && ln "$single_or_paired.reverse_pe" "$single_or_paired.forward_pe.name"_2.fastq &&
18 kat sect 'db.fasta'
19 "$single_or_paired.forward_pe.name"_1.fastq "$single_or_paired.forward_pe.name"_2.fastq
20 #else
21 ln "$single_or_paired.fastq_collection.forward" "$single_or_paired.fastq_collection.forward.name"_1.fastq && ln "$single_or_paired.fastq_collection.reverse" "$single_or_paired.fastq_collection.forward.name"_2.fastq &&
22 kat sect 'db.fasta'
23 "$single_or_paired.fastq_collection.forward.name"_1.fastq "$single_or_paired.fastq_collection.forward.name"_2.fastq
24 #end if
25 --threads \${GALAXY_SLOTS:-4}
26 -o reads
27
28 ]]></command>
29 <inputs>
30 <conditional name="single_or_paired">
31 <param name="type" type="select" label="Read type">
32 <option value="single">Single-end</option>
33 <option value="paired">Paired-end</option>
34 <option value="collection">Collection Paired-end</option>
35 </param>
36 <when value="single">
37 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
38 </when>
39 <when value="paired">
40 <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
41 <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
42 </when>
43 <when value="collection">
44 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" />
45 </when>
46 </conditional>
47 <param name="db" type="data" format="fasta" label="Fasta file of targeted regions"/>
48 </inputs>
49 <outputs>
50 <data format="tabular" name="reads" label='Reads' from_work_dir="reads-stats.tsv" />
51 </outputs>
52 <tests>
53 <test>
54 <param name="input" value="input.fastq" />
55 <param name="db" value="db.fasta" />
56 <output file="matched.fastq" ftype="fastqsanger" name="reads" />
57 </test>
58 </tests>
59 <help><![CDATA[
60 http://kat.readthedocs.io/en/latest/using.html#filtering-tools
61 ]]>
62
63 </help>
64 <citations>
65 </citations>
66 </tool>