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comparison fastk.xml @ 0:794d07dc1c68 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 9257c0d48c94f40919d29e48f210c58099608aa7
author iuc
date Mon, 04 Nov 2024 14:20:00 +0000
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children b446c2f40b60
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-1:000000000000 0:794d07dc1c68
1 <tool id="fastk_fastk" name="FastK" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
2 <description>A k-mer counter for high-quality assembly datasets</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p outfiles/ktabfiles &&
9 #if $infile.is_of_type("fastq"):
10 #set INPUTFILE="input.fastq"
11 #elif $infile.is_of_type("fastq.gz"):
12 #set INPUTFILE="input.fastq.gz"
13 #else
14 #set INPUTFILE="input."+$infile.ext
15 #end if
16 ln -s '$infile' $INPUTFILE &&
17 FastK $INPUTFILE
18 -k$kmer_size
19 #if $sorted_table.sorted_table_option == 'yes_with_default':
20 -t
21 #elif $sorted_table.sorted_table_option == 'yes_with_custom':
22 -t$sorted_table_cutoff
23 #end if
24 -T\${GALAXY_SLOTS:-8} -Noutfiles/output -Poutfiles/ktabfiles
25 #if $sorted_table.sorted_table_option == 'yes_with_default':
26 && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_default} LIST > '$tabex_hist'
27 && cp outfiles/.*.ktab* outfiles/ktabfiles
28 && cp outfiles/*.ktab outfiles/ktabfiles
29 #elif $sorted_table.sorted_table_option == 'yes_with_custom':
30 && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_custom} LIST > '$tabex_hist'
31 && cp outfiles/.*.ktab* outfiles/ktabfiles
32 && cp outfiles/*.ktab outfiles/ktabfiles
33 #end if
34 && tar -c -f fastk.tar ./outfiles/
35 ]]></command>
36 <inputs>
37 <param name="infile" type="data" format="fasta,fasta.gz,fastq,fastq.gz,cram,unsorted.bam,sam" label="Input file"/>
38 <param name="kmer_size" argument="-k" type="integer" min="5" max="50" value="40" label="Enter desired k-mer size" help="Default: 40"/>
39 <conditional name="sorted_table">
40 <param name="sorted_table_option" type="select" label="Sort table" help="Do you want a sorted table of all canonical k-mers and their counts? The sorted table is sorted lexicographically on the k-mer where a &lt; c &lt; g &lt; t.">
41 <option value="no">No</option>
42 <option value="yes_with_default">Yes, Default sorted </option>
43 <option value="yes_with_custom">Yes, Custom sorted </option>
44 </param>
45 <when value="no"/>
46 <when value="yes_with_default">
47 <param name="tabex_threshold_for_default" argument="-t" type="integer" value="5" min="1" label="Tabex count threshold" help="Trim all k-mers with counts less than threshold"/>
48 </when>
49 <when value="yes_with_custom">
50 <param name="sorted_table_cutoff" type="integer" min="2" value="10" label="Enter sorted table cutoff value"/>
51 <param name="tabex_threshold_for_custom" argument="-t" type="integer" value="5" min="1" label="Tabex count threshold" help="Trim all k-mers with counts less than threshold"/>
52 </when>
53 </conditional>
54 </inputs>
55 <outputs>
56 <data name="fastk_out" format="tar" from_work_dir="fastk.tar" label="${tool.name} on ${on_string}: FastK files"/>
57 <data name="fastk_hist_out" format="fastk_hist" from_work_dir="outfiles/output.hist" label="${tool.name} on ${on_string}: FastK hist"/>
58 <data name="fastk_ktab_out" format="fastk_ktab" from_work_dir="outfiles/ktabfiles/output.ktab" label="${tool.name} on ${on_string}: FastK ktab">
59 <filter> sorted_table['sorted_table_option'] != 'no' </filter>
60 </data>
61 <data name="tabex_hist" format="txt" label="${tool.name} on ${on_string}: Tabex output">
62 <filter> sorted_table['sorted_table_option'] != 'no' </filter>
63 </data>
64 </outputs>
65 <tests>
66 <!-- TEST 1 -->
67 <test expect_num_outputs="2">
68 <param name="infile" value="input01.fasta.gz"/>
69 <output name="fastk_out" ftype="tar">
70 <assert_contents>
71 <has_archive_member path="./outfiles/output.hist"/>
72 </assert_contents>
73 </output>
74 </test>
75 <!-- TEST 2 -->
76 <test expect_num_outputs="4">
77 <param name="infile" value="input01.fasta.gz"/>
78 <conditional name="sorted_table">
79 <param name="sorted_table_option" value="yes_with_default"/>
80 </conditional>
81 <output name="fastk_out" ftype="tar">
82 <assert_contents>
83 <has_archive_member path="./outfiles/output.hist"/>
84 <has_archive_member path="./outfiles/ktabfiles/output.ktab"/>
85 </assert_contents>
86 </output>
87 <output name="tabex_hist" file="test02.tabex.txt"/>
88 </test>
89 <!-- TEST 3 -->
90 <test expect_num_outputs="4">
91 <param name="infile" value="input01.fasta.gz"/>
92 <conditional name="sorted_table">
93 <param name="sorted_table_option" value="yes_with_custom"/>
94 <param name="sorted_table_cutoff" value="5"/>
95 </conditional>
96 <output name="fastk_out" ftype="tar">
97 <assert_contents>
98 <has_archive_member path="./outfiles/output.hist"/>
99 <has_archive_member path="./outfiles/ktabfiles/output.ktab"/>
100 </assert_contents>
101 </output>
102 <output name="tabex_hist" file="test03.tabex.txt"/>
103 </test>
104 </tests>
105 <help><![CDATA[
106 FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode.
107
108 The input data can be in CRAM, BAM, SAM, fasta, or fastq files.
109
110 FastK produces the following outputs:
111
112 1. FastK hist: file in binary format containing histogram information detailing the frequency of occurrence for each k‑mer within the dataset.
113
114 2. A Tabex txt file comprising a table of k‑mer/count pairs, sorted lexicographically on the k‑mer sequence, followingthe order a < c < g < t
115
116 3. A tar file comprising of hidden .ktab files that can be used for downstream FASTK tools.
117
118
119 ]]></help>
120 <expand macro="citations"/>
121 </tool>