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comparison fastk.xml @ 2:b446c2f40b60 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 9412d515121c3b2d55d3b2040dc04869866eae66
author iuc
date Fri, 06 Dec 2024 15:47:31 +0000
parents 794d07dc1c68
children b7b4d73c7f66
comparison
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1:226636a67bc1 2:b446c2f40b60
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p outfiles/ktabfiles && 8 mkdir -p ktabfiles &&
9 #if $infile.is_of_type("fastq"): 9 #if $infile.is_of_type("fastq"):
10 #set INPUTFILE="input.fastq" 10 #set INPUTFILE="input.fastq"
11 #elif $infile.is_of_type("fastq.gz"): 11 #elif $infile.is_of_type("fastq.gz"):
12 #set INPUTFILE="input.fastq.gz" 12 #set INPUTFILE="input.fastq.gz"
13 #else 13 #else
19 #if $sorted_table.sorted_table_option == 'yes_with_default': 19 #if $sorted_table.sorted_table_option == 'yes_with_default':
20 -t 20 -t
21 #elif $sorted_table.sorted_table_option == 'yes_with_custom': 21 #elif $sorted_table.sorted_table_option == 'yes_with_custom':
22 -t$sorted_table_cutoff 22 -t$sorted_table_cutoff
23 #end if 23 #end if
24 -T\${GALAXY_SLOTS:-8} -Noutfiles/output -Poutfiles/ktabfiles 24 -T\${GALAXY_SLOTS:-8} -Noutput -Pktabfiles
25 #if $sorted_table.sorted_table_option == 'yes_with_default': 25 #if $sorted_table.sorted_table_option == 'yes_with_default':
26 && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_default} LIST > '$tabex_hist' 26 && Tabex output.ktab -t${sorted_table.tabex_threshold_for_default} LIST > '$tabex_hist'
27 && cp outfiles/.*.ktab* outfiles/ktabfiles 27 && cp .*.ktab* ktabfiles/
28 && cp outfiles/*.ktab outfiles/ktabfiles 28 && cp *.ktab ktabfiles/
29 #elif $sorted_table.sorted_table_option == 'yes_with_custom': 29 #elif $sorted_table.sorted_table_option == 'yes_with_custom':
30 && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_custom} LIST > '$tabex_hist' 30 && Tabex output.ktab -t${sorted_table.tabex_threshold_for_custom} LIST > '$tabex_hist'
31 && cp outfiles/.*.ktab* outfiles/ktabfiles 31 && cp *.ktab* ktabfiles/
32 && cp outfiles/*.ktab outfiles/ktabfiles 32 && cp *.ktab ktabfiles/
33 #end if 33 #end if
34 && tar -c -f fastk.tar ./outfiles/ 34 && tar -cf fastk.tar ktabfiles/
35 ]]></command> 35 ]]></command>
36 <inputs> 36 <inputs>
37 <param name="infile" type="data" format="fasta,fasta.gz,fastq,fastq.gz,cram,unsorted.bam,sam" label="Input file"/> 37 <param name="infile" type="data" format="fasta,fasta.gz,fastq,fastq.gz,cram,unsorted.bam,sam" label="Input file"/>
38 <param name="kmer_size" argument="-k" type="integer" min="5" max="50" value="40" label="Enter desired k-mer size" help="Default: 40"/> 38 <param name="kmer_size" argument="-k" type="integer" min="5" max="50" value="40" label="Enter desired k-mer size" help="Default: 40"/>
39 <conditional name="sorted_table"> 39 <conditional name="sorted_table">
52 </when> 52 </when>
53 </conditional> 53 </conditional>
54 </inputs> 54 </inputs>
55 <outputs> 55 <outputs>
56 <data name="fastk_out" format="tar" from_work_dir="fastk.tar" label="${tool.name} on ${on_string}: FastK files"/> 56 <data name="fastk_out" format="tar" from_work_dir="fastk.tar" label="${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 ${on_string}: FastK hist"/> 57 <data name="fastk_hist_out" format="fastk_hist" from_work_dir="output.hist" label="${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 ${on_string}: FastK ktab"> 58 <data name="fastk_ktab_out" format="fastk_ktab" from_work_dir="ktabfiles/output.ktab" label="${tool.name} on ${on_string}: FastK ktab">
59 <filter> sorted_table['sorted_table_option'] != 'no' </filter> 59 <filter> sorted_table['sorted_table_option'] != 'no' </filter>
60 </data> 60 </data>
61 <data name="tabex_hist" format="txt" label="${tool.name} on ${on_string}: Tabex output"> 61 <data name="tabex_hist" format="txt" label="${tool.name} on ${on_string}: Tabex output">
62 <filter> sorted_table['sorted_table_option'] != 'no' </filter> 62 <filter> sorted_table['sorted_table_option'] != 'no' </filter>
63 </data> 63 </data>
64 </outputs> 64 </outputs>
65 <tests> 65 <tests>
66 <!-- TEST 1 --> 66 <!-- TEST 1 -->
67 <test expect_num_outputs="2"> 67 <test expect_num_outputs="2">
68 <param name="infile" value="input01.fasta.gz"/> 68 <param name="infile" value="input01.fasta.gz"/>
69 <param name="kmer_size" value="40"/>
70 <output name="fastk_hist_out" file="test01.hist" ftype="fastk_hist"/>
69 <output name="fastk_out" ftype="tar"> 71 <output name="fastk_out" ftype="tar">
70 <assert_contents> 72 <assert_contents>
71 <has_archive_member path="./outfiles/output.hist"/> 73 <has_archive_member path="ktabfiles"/>
72 </assert_contents> 74 </assert_contents>
73 </output> 75 </output>
74 </test> 76 </test>
75 <!-- TEST 2 --> 77 <!-- TEST 2 -->
76 <test expect_num_outputs="4"> 78 <test expect_num_outputs="4">
77 <param name="infile" value="input01.fasta.gz"/> 79 <param name="infile" value="input01.fasta.gz"/>
78 <conditional name="sorted_table"> 80 <conditional name="sorted_table">
79 <param name="sorted_table_option" value="yes_with_default"/> 81 <param name="sorted_table_option" value="yes_with_default"/>
80 </conditional> 82 </conditional>
83 <output name="fastk_hist_out" file="test02.hist" ftype="fastk_hist"/>
81 <output name="fastk_out" ftype="tar"> 84 <output name="fastk_out" ftype="tar">
82 <assert_contents> 85 <assert_contents>
83 <has_archive_member path="./outfiles/output.hist"/> 86 <has_archive_member path="ktabfiles/output.ktab"/>
84 <has_archive_member path="./outfiles/ktabfiles/output.ktab"/>
85 </assert_contents> 87 </assert_contents>
86 </output> 88 </output>
87 <output name="tabex_hist" file="test02.tabex.txt"/> 89 <output name="tabex_hist" file="test02.tabex.txt"/>
88 </test> 90 </test>
89 <!-- TEST 3 --> 91 <!-- TEST 3 -->
91 <param name="infile" value="input01.fasta.gz"/> 93 <param name="infile" value="input01.fasta.gz"/>
92 <conditional name="sorted_table"> 94 <conditional name="sorted_table">
93 <param name="sorted_table_option" value="yes_with_custom"/> 95 <param name="sorted_table_option" value="yes_with_custom"/>
94 <param name="sorted_table_cutoff" value="5"/> 96 <param name="sorted_table_cutoff" value="5"/>
95 </conditional> 97 </conditional>
98 <output name="fastk_hist_out" file="test03.hist" ftype="fastk_hist"/>
96 <output name="fastk_out" ftype="tar"> 99 <output name="fastk_out" ftype="tar">
97 <assert_contents> 100 <assert_contents>
98 <has_archive_member path="./outfiles/output.hist"/> 101 <has_archive_member path="ktabfiles/output.ktab"/>
99 <has_archive_member path="./outfiles/ktabfiles/output.ktab"/>
100 </assert_contents> 102 </assert_contents>
101 </output> 103 </output>
102 <output name="tabex_hist" file="test03.tabex.txt"/> 104 <output name="tabex_hist" file="test03.tabex.txt"/>
103 </test> 105 </test>
104 </tests> 106 </tests>
113 115
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 116 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
115 117
116 3. A tar file comprising of hidden .ktab files that can be used for downstream FASTK tools. 118 3. A tar file comprising of hidden .ktab files that can be used for downstream FASTK tools.
117 119
118
119 ]]></help> 120 ]]></help>
120 <expand macro="citations"/> 121 <expand macro="citations"/>
121 </tool> 122 </tool>