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planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
author galaxy-australia
date Tue, 01 Oct 2024 04:06:26 +0000
parents ca2743037241
children
comparison
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0:ca2743037241 1:c7fda6e88567
1 <tool id="kmc" name="KMC Counter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > 1 <tool id="kmc" name="KMC Counter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>K-mer counting and filtering of reads</description> 2 <description>K-mer counting and filtering of reads</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
3 <xrefs> 6 <xrefs>
4 <xref type='bio.tools'>kmc</xref> 7 <xref type='bio.tools'>kmc</xref>
5 </xrefs> 8 </xrefs>
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command><![CDATA[ 12 <command><![CDATA[
13 kmc 13 mkdir output &&
14 #if $data_type.select == 'individual'
15 #for $input_file in $data_type.individual_file
16 #if $input_file.is_of_type("fastq","fastq.gz","fastqsanger.gz"):
17 #if $input_file.ext.endswith(".gz")
18 #set $ext='.fastq.gz'
19 #else
20 #set $ext='.fastq'
21 #end if
22 ln -s '$input_file' 'in$ext' &&
23 #elif $input_file.is_of_type("fasta","fasta.gz"):
24 #if $input_file.ext.endswith(".gz")
25 #set $ext='.fasta.gz'
26 #else
27 #set $ext='.fasta'
28 #end if
29 ln -s '$input_file' 'in$ext' &&
30 #elif $input_file.is_of_type("bam"):
31 ln -s '$input_file' in.bam &&
32 #elif $input_file.is_of_type("kmc_suf"):
33 #if $input_file.ext.endswith(".kmc_suf")
34 #set $suf_ext='.kmc_suf'
35 #end if
36 #if $input_file.ext.endswith(".kmc_pre")
37 #set $pre_ext='.kmc_pre'
38 #end if
39 ln -s '$input_file' 'in$suf_ext' &&
40 ln -s '$input_file' 'in$pre_ext' &&
41 #end if
42 #end for
43 #else
44 mkdir input_dir &&
45 #import re
46 #for $input_file in $data_type.collection_file
47 #if $input_file.is_of_type("fastq","fastq.gz","fastqsanger.gz"):
48 #if $input_file.ext.endswith(".gz")
49 #set $ext='.fastq.gz'
50 #else
51 #set $ext='.fastq'
52 #end if
53 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
54 ln -s '$input_file' 'input_dir/${identifier}' &&
55 #elif $input_file.is_of_type("fasta","fasta.gz"):
56 #if $input_file.ext.endswith(".gz")
57 #set $ext='.fasta.gz'
58 #else
59 #set $ext='.fasta'
60 #end if
61 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
62 ln -s '$input_file' 'input_dir/${identifier}' &&
63 #elif $input_file.is_of_type("bam"):
64 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
65 ln -s '$input_file' 'input_dir/${identifier}' &&
66 #elif $input_file.is_of_type("kmc_suf"):
67 #if $input_file.ext.endswith(".kmc_suf")
68 #set $suf_ext='.kmc_suf'
69 #end if
70 #if $input_file.ext.endswith(".kmc_pre")
71 #set $pre_ext='.kmc_pre'
72 #end if
73 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
74 ln -s '$input_file' 'input_dir/${identifier}' &&
75 ln -s '$input_file' 'input_dir/${identifier}' &&
76 #end if
77 #end for
78 ls -ld input_dir/* | awk '{print $9}' >> files.list &&
79 #end if
80
81 kmc
14 -t\${GALAXY_SLOTS:-4} 82 -t\${GALAXY_SLOTS:-4}
15 #if $params.k: 83 #if $params.k:
16 -k'$params.k' 84 -k'$params.k'
17 #end if 85 #end if
18 #if $params.m: 86 -m\${GALAXY_MEMORY_GB:-4}
19 -m'$params.m'
20 #end if
21 #if $params.j: 87 #if $params.j:
22 -j'$statistic' 88 -j'$statistic'
23 #end if 89 #end if
24 #if $params.exclude_length: 90 #if $params.p:
25 -ci'$params.exclude_length' 91 -p'$params.p'
26 #end if 92 #end if
27 #if $params.max_counter_value: 93 #if $params.ci:
28 -cs'$params.max_counter_value' 94 -ci'$params.ci'
29 #end if 95 #end if
30 #if $input_file.is_of_type("fastq"): 96 #if $params.cs:
31 -fq 97 -cs'$params.cs'
32 #elif $input_file.is_of_type("fasta"): 98 #end if
33 -fm 99 #if $params.cx:
100 -cx'$params.cx'
101 #end if
102 #if $input_file.is_of_type("fastq","fastq.gz","fastqsanger.gz"):
103 -fq
104 #elif $input_file.is_of_type("fasta","fasta.gz"):
105 #if $data_type.select == "individual":
106 -fa
107 #else
108 -fm
109 #end if
34 #elif $input_file.is_of_type("bam"): 110 #elif $input_file.is_of_type("bam"):
35 -fbam 111 -fbam
36 #elif $input_file.is_of_type("kmc_suf"): 112 #elif $input_file.is_of_type("kmc_suf"):
37 -fkmc 113 -fkmc
114 #end if
115
116 #if $input_file.is_of_type('fastq.gz','fasta.gz','fastqsanger.gz'):
117 -f
38 #end if 118 #end if
39 $input_file 119
40 db 120 #if $data_type.select == 'individual'
41 . 121 #if $input_file.is_of_type("fastq","fastq.gz","fastqsanger.gz"):
122 #if $input_file.ext.endswith(".gz")
123 in.fastq.gz
124 #else
125 in.fastq
126 #end if
127 #elif $input_file.is_of_type("fasta","fasta.gz"):
128 #if $input_file.ext.endswith(".gz")
129 in.fasta.gz
130 #else
131 in.fasta
132 #end if
133 #elif $input_file.is_of_type("bam"):
134 in.bam
135 #end if
136 #else
137 @files.list
138 #end if
139 output/kmer_"$params.k"
140 .
42 141
43 ]]></command> 142 ]]></command>
44 <inputs> 143 <inputs>
45 <expand macro="macro_input" /> 144 <expand macro="macro_input" />
46 <section name="params" title="parameter" expanded="false"> 145 <section name="params" title="parameter" expanded="false">
47 <param argument="-k" type="integer" value="25" label="k-mer length (k from 1 to 256; default: 25)" /> 146 <param argument="-k" type="integer" value="25" label="k-mer length (k from 1 to 256; default: 25)" />
48 <param argument="-m" type="integer" value="12" label="max amount of RAM in GB (from 1 to 1024); default: 12" /> 147 <param argument="-p" type="integer" value="9" label="signature length (5, 6, 7, 8, 9, 10, 11); default: 9"/>
49 <param name="signature_length" arguments="-p" type="integer" value="9" label="signature length (5, 6, 7, 8, 9, 10, 11); default: 9"/> 148 <param argument="-ci" type="integer" value="2" label="exclude k-mers occurring less than [value] times (default: 2)"/>
50 <param name="exclude_length" arguments="-ci" type="integer" value="2" label="exclude k-mers occurring less than [value] times (default: 2)"/> 149 <param argument="-cs" type="integer" value="255" label="maximal value of a counter (default: 255)"/>
51 <param name="max_counter_value" arguments="-cs" type="integer" value="255" label="maximal value of a counter (default: 255)"/> 150 <param argument="-cx" type="integer" value="1000000000" label="xclude k-mers occurring more of than [value] times (default: 1e9)"/>
52 <param name="exclude_kmer_occurence" arguments="-cx" type="integer" value="1000000000" label="xclude k-mers occurring more of than [value] times (default: 1e9)"/>
53 <param argument="-j" type="boolean" truevalue="-j" falsevalue="" checked="True" label="file name with execution summary in JSON format"/> 151 <param argument="-j" type="boolean" truevalue="-j" falsevalue="" checked="True" label="file name with execution summary in JSON format"/>
54 </section> 152 </section>
55 </inputs> 153 </inputs>
56 <outputs> 154 <outputs>
57 <data format="json" name="statistic" label="${tool.name} on ${on_string}"> 155 <data name="statistic" format="json" label="${tool.name} on ${on_string}">
58 <filter>params['j']</filter> 156 <filter>params['j']</filter>
59 </data> 157 </data>
60 <collection name="kmc_db" type="list" label="${tool.name} on ${on_string}: kmc db"> 158 <collection name="kmc_db" type="list" label="${tool.name} on ${on_string}: kmc db">
61 <data format="binary" name="db.kmc_suf" label="${tool.name} on ${on_string}" from_work_dir="db.kmc_suf" /> 159 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="output" format="binary" />
62 <data format="binary" name="db.kmc_pre" label="${tool.name} on ${on_string}" from_work_dir="db.kmc_pre" />
63 </collection> 160 </collection>
64 </outputs> 161 </outputs>
65
66 <tests> 162 <tests>
67 <test> 163 <test expect_num_outputs="2">
68 <!-- #1 test fastq with common parameters --> 164 <!-- #1 test individual fasta file -->
69 <param name="input_file" value="F3D0_R1.fastq" ftype="fastq"/> 165 <param name="individual_file" value="test.fasta.gz" ftype="fasta.gz"/>
166 <param name="k" value="27" />
167 <param name="ci" value="2" />
168 <param name="cs" value="255" />
169 <output_collection name="kmc_db" type="list">
170 <element name="kmer_27.kmc_pre" file="kmer_27.kmc_pre" ftype="binary" />
171 <element name="kmer_27.kmc_suf" file="kmer_27.kmc_suf" ftype="binary" />
172 </output_collection>
173 <output name="statistic" ftype="json">
174 <assert_contents>
175 <has_text text="1st_stage"/>
176 <has_text text="2nd_stage"/>
177 <has_text text="Stats"/>
178 </assert_contents>
179 </output>
180 </test>
181 <!-- output file is too large for testing; comment out to test on local machine with update_test_data option -->
182 <!-- <test expect_num_outputs="2"> -->
183 <!-- #2 test individual fastq file -->
184 <!-- <param name="individual_file" value="filtered_1.fastq" ftype="fastq"/>
70 <param name="k" value="25" /> 185 <param name="k" value="25" />
71 <param name="m" value="12" />
72 <param name="p" value="9" /> 186 <param name="p" value="9" />
73 <param name="ci" value="2" /> 187 <param name="ci" value="2" />
74 <param name="cs" value="255" /> 188 <param name="cs" value="255" />
75 <output name="db.kmc_suf" file="db.kmc_suf" ftype="binary" /> 189 <output_collection name="kmc_db" type="list">
76 <output name="db.kmc_pre" file="db.kmc_pre" ftype="binary" /> 190 <element name="kmer_25.kmc_pre" file="kmer_25.kmc_pre" ftype="binary" />
77 </test> 191 <element name="kmer_25.kmc_suf" file="kmer_25.kmc_suf" ftype="binary" />
78 <test> 192 </output_collection>
79 <!-- #2 test fasta with common parameters --> 193 <output name="statistic" ftype="json">
80 <param name="input_file" value="contigs.fa" ftype="fasta"/> 194 <assert_contents>
81 <param name="k" value="27" /> 195 <has_text text="1st_stage"/>
82 <param name="m" value="24" /> 196 <has_text text="2nd_stage"/>
197 <has_text text="Stats"/>
198 </assert_contents>
199 </output>
200 </test> -->
201 <!-- output file is too large for testing; comment out to test on local machine -->
202 <!-- <test expect_num_outputs="2"> -->
203 <!-- #3 test collection fastq with common parameters -->
204 <!-- <param name="k" value="29" />
205 <param name="m" value="12" />
206 <param name="p" value="9" />
83 <param name="ci" value="2" /> 207 <param name="ci" value="2" />
84 <param name="cs" value="255" /> 208 <param name="cs" value="255" />
85 <param name="fm" value="-fm" /> 209 <conditional name="data_type">
86 <output name="contig_kmer27.kmc_suf" file="contig_kmer27.kmc_suf" ftype="binary" /> 210 <param name="select" value="collection"/>
87 <output name="contig_kmer27.kmc_pre" file="contig_kmer27.kmc_pre" ftype="binary" /> 211 <param name="collection_file">
88 </test> 212 <collection type="list">
213 <element name="filtered_1.fastq" value="filtered_1.fastq" ftype="fastq"/>
214 <element name="filtered_2.fastq" value="filtered_2.fastq" ftype="fastq"/>
215 </collection>
216 </param>
217 </conditional>
218 <output_collection name="kmc_db">
219 <element name="kmer_29.kmc_suf" file="kmer_29.kmc_suf" ftype="binary" />
220 <element name="kmer_29.kmc_pre" file="kmer_29.kmc_pre" ftype="binary" />
221 </output_collection>
222 <output name="statistic" ftype="json">
223 <assert_contents>
224 <has_text text="1st_stage"/>
225 <has_text text="2nd_stage"/>
226 <has_text text="Stats"/>
227 </assert_contents>
228 </output>
229 </test>
230 -->
89 </tests> 231 </tests>
90 <help><![CDATA[ 232 <help><![CDATA[
91 233
92 .. class:: infomark 234 .. class:: infomark
93 235