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comparison kat_sect.xml @ 3:624f99fe1705 draft default tip

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planemo upload commit cf7305a207096e24bedddb0cb55bed86a6b7cd6b
author nml
date Wed, 15 Mar 2017 13:56:48 -0400
parents 7f59ee641f70
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2:7f59ee641f70 3:624f99fe1705
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.1"> 2 <tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.2">
3 <description> Estimates the coverage of each sequence in a file using K-mers from another sequence file(s).</description> 3 <description> Estimates the coverage of each sequence in a file using K-mers from another sequence file(s).</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">sect</token> 5 <token name="@EXECUTABLE@">sect</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
10 <expand macro="version_command" /> 10 <expand macro="version_command" />
11 <command><![CDATA[ 11 <command><![CDATA[
12 12
13 cp "$db" db.fasta && 13 cp "$db" db.fasta &&
14 #if $single_or_paired.type == "single" 14 #if $single_or_paired.type == "single"
15 ln "$input_se" "$single_or_paired.input_se.element_identifier".fastq && 15 ln "$input_se" read.fastq &&
16 kat sect 'db.fasta' 16 kat sect 'db.fasta'
17 "$single_or_paired.input_se.element_identifier".fastq 17 read.fastq
18 #elif $single_or_paired.type == "paired" 18 #elif $single_or_paired.type == "paired"
19 ln "$single_or_paired.forward_pe" "$single_or_paired.forward_pe.name"_1.fastq && ln "$single_or_paired.reverse_pe" "$single_or_paired.forward_pe.name"_2.fastq && 19 ln "$single_or_paired.forward_pe" read_1.fastq && ln "$single_or_paired.reverse_pe" read_2.fastq &&
20 kat sect 'db.fasta' 20 kat sect 'db.fasta'
21 "$single_or_paired.forward_pe.name"_1.fastq "$single_or_paired.forward_pe.name"_2.fastq 21 read_1.fastq read_2.fastq
22 #else 22 #else
23 ln "$single_or_paired.fastq_collection.forward" "$single_or_paired.fastq_collection.forward.name"_1.fastq && ln "$single_or_paired.fastq_collection.reverse" "$single_or_paired.fastq_collection.forward.name"_2.fastq && 23 ln "$single_or_paired.fastq_collection.forward" read_1.fastq && ln "$single_or_paired.fastq_collection.reverse" read_2.fastq &&
24 kat sect 'db.fasta' 24 kat sect 'db.fasta'
25 "$single_or_paired.fastq_collection.forward.name"_1.fastq "$single_or_paired.fastq_collection.forward.name"_2.fastq 25 read_1.fastq read_2.fastq
26 #end if 26 #end if
27 27
28 @THREADS@ 28 @THREADS@
29 29
30 --mer_len $kmer 30 --mer_len $kmer