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planemo upload commit 41caf97a4a9a7928318af8b24601f84a380fe2db
author galaxytrakr
date Fri, 18 Sep 2026 12:26:54 +0000
parents 56b71adcaba7
children
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7:56b71adcaba7 8:2b1f3db24c25
1 <tool id="mitokmer" name="mitoKmer" version="2.0+galaxy0.23" profile="21.05"> 1 <tool id="mitokmer" name="mitoKmer" version="2.0+galaxy0.24" profile="21.05">
2 <description>Identify metagenomic mitochondrial reads by k-mer database matching</description> 2 <description>Identify metagenomic mitochondrial reads by k-mer database matching</description>
3 <requirements> 3 <requirements>
4 <container type="docker">quay.io/galaxytrakr/mitokmer:e57a559</container> 4 <container type="docker">quay.io/galaxytrakr/mitokmer:e57a559</container>
5 </requirements> 5 </requirements>
6 6
19 19
20 ## ── Symlink kmerread7 binary into working directory ─────────────────── 20 ## ── Symlink kmerread7 binary into working directory ───────────────────
21 ln -sf /usr/local/bin/kmerread7 ./kmerread7 && 21 ln -sf /usr/local/bin/kmerread7 ./kmerread7 &&
22 22
23 ## ── Stage input reads and build jobs file ──────────────────────────── 23 ## ── Stage input reads and build jobs file ────────────────────────────
24 #if $reads.reads_type == "single" 24 #if $reads.reads_type == "single_file"
25 mkdir -p ./reads &&
26 #set sample_name = re.sub('[^\w\-_.]', '_', $reads.input.name)
27 #set ext = $fix_ext($reads.input.ext)
28 #set fname = re.sub('[^\w\-_.]', '_', $reads.input.element_identifier) + '.' + $ext
29 ln -sf '$reads.input' './reads/${fname}' &&
30 printf '%s\t1\n' '${sample_name}' > ./jobs7m/jobs7m.txt &&
31 printf '%s\n' './reads/${fname}' >> ./jobs7m/jobs7m.txt &&
32 #else if $reads.reads_type == "single"
25 mkdir -p ./reads && 33 mkdir -p ./reads &&
26 #set sample_name = re.sub('[^\w\-_.]', '_', $reads.input.name) 34 #set sample_name = re.sub('[^\w\-_.]', '_', $reads.input.name)
27 #set read_count = 0 35 #set read_count = 0
28 #for $read in $reads.input 36 #for $read in $reads.input
29 #set ext = $fix_ext($read.ext) 37 #set ext = $fix_ext($read.ext)
72 </options> 80 </options>
73 </param> 81 </param>
74 82
75 <conditional name="reads"> 83 <conditional name="reads">
76 <param name="reads_type" type="select" label="Input read type"> 84 <param name="reads_type" type="select" label="Input read type">
85 <option value="single_file">Single FASTA or FASTQ dataset</option>
77 <option value="single">Single-end or unpaired reads / FASTA (list collection)</option> 86 <option value="single">Single-end or unpaired reads / FASTA (list collection)</option>
78 <option value="paired">Paired-end reads (paired collection)</option> 87 <option value="paired">Paired-end reads (paired collection)</option>
79 </param> 88 </param>
89 <when value="single_file">
90 <param name="input" type="data"
91 format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fasta,fasta.gz"
92 label="Input FASTA or FASTQ dataset"
93 help="Provide a single FASTA or FASTQ file from your history." />
94 </when>
80 <when value="single"> 95 <when value="single">
81 <param name="input" type="data_collection" collection_type="list" 96 <param name="input" type="data_collection" collection_type="list"
82 format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fasta,fasta.gz" 97 format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fasta,fasta.gz"
83 label="Input reads (FASTQ or FASTA, gzipped or plain)" 98 label="Input reads (FASTQ or FASTA, gzipped or plain)"
84 help="Provide one or more single-end or unpaired read files as a Galaxy 99 help="Provide one or more single-end or unpaired read files as a Galaxy
99 <outputs> 114 <outputs>
100 <data name="results_csv" format="csv" label="mitoKmer results for ${on_string}" /> 115 <data name="results_csv" format="csv" label="mitoKmer results for ${on_string}" />
101 </outputs> 116 </outputs>
102 117
103 <tests> 118 <tests>
104 <!-- Test 1: paired-end FASTQ via paired collection --> 119 <!-- Test 1: single FASTA dataset -->
120 <test>
121 <param name="probe_db" value="mitoch_probes_sample" />
122 <conditional name="reads">
123 <param name="reads_type" value="single_file" />
124 <param name="input" value="test/Plodia_assembly.fasta" ftype="fasta" />
125 </conditional>
126 <output name="results_csv">
127 <assert_contents>
128 <has_text text="Plodia" />
129 </assert_contents>
130 </output>
131 </test>
132 <!-- Test 2: paired-end FASTQ via paired collection -->
105 <test> 133 <test>
106 <param name="probe_db" value="mitoch_probes_sample" /> 134 <param name="probe_db" value="mitoch_probes_sample" />
107 <conditional name="reads"> 135 <conditional name="reads">
108 <param name="reads_type" value="paired" /> 136 <param name="reads_type" value="paired" />
109 <param name="input"> 137 <param name="input">
117 <assert_contents> 145 <assert_contents>
118 <has_text text="Plodia" /> 146 <has_text text="Plodia" />
119 </assert_contents> 147 </assert_contents>
120 </output> 148 </output>
121 </test> 149 </test>
122 <!-- Test 2: single-end FASTQ via list collection --> 150 <!-- Test 3: single-end FASTQ via list collection -->
123 <test> 151 <test>
124 <param name="probe_db" value="mitoch_probes_sample" /> 152 <param name="probe_db" value="mitoch_probes_sample" />
125 <conditional name="reads"> 153 <conditional name="reads">
126 <param name="reads_type" value="single" /> 154 <param name="reads_type" value="single" />
127 <param name="input"> 155 <param name="input">
134 <assert_contents> 162 <assert_contents>
135 <has_text text="Plodia" /> 163 <has_text text="Plodia" />
136 </assert_contents> 164 </assert_contents>
137 </output> 165 </output>
138 </test> 166 </test>
139 <!-- Test 3: single FASTA via list collection --> 167 <!-- Test 4: FASTA list collection -->
140 <test> 168 <test>
141 <param name="probe_db" value="mitoch_probes_sample" /> 169 <param name="probe_db" value="mitoch_probes_sample" />
142 <conditional name="reads"> 170 <conditional name="reads">
143 <param name="reads_type" value="single" /> 171 <param name="reads_type" value="single" />
144 <param name="input"> 172 <param name="input">
176 of ``.txt`` files. 204 of ``.txt`` files.
177 205
178 **Input read type** 206 **Input read type**
179 Choose the input mode that matches your data: 207 Choose the input mode that matches your data:
180 208
209 *Single FASTA or FASTQ dataset*
210 Provide a single FASTA or FASTQ file directly from your history.
211 This is the simplest option for a single assembled sequence or
212 single-end read file.
213
181 *Single-end or unpaired reads / FASTA (list collection)* 214 *Single-end or unpaired reads / FASTA (list collection)*
182 Provide a Galaxy **list** collection containing one or more FASTQ 215 Provide a Galaxy **list** collection containing one or more FASTQ
183 (``fastqsanger``, ``fastqsanger.gz``) or FASTA (``fasta``, 216 (``fastqsanger``, ``fastqsanger.gz``) or FASTA (``fasta``,
184 ``fasta.gz``) files. Use this for single-end sequencing data or 217 ``fasta.gz``) files. Use this for single-end sequencing data or
185 assembled FASTA sequences. 218 multiple assembled FASTA sequences processed together.
186 219
187 *Paired-end reads (paired collection)* 220 *Paired-end reads (paired collection)*
188 Provide a Galaxy **paired** collection where the forward (R1) and 221 Provide a Galaxy **paired** collection where the forward (R1) and
189 reverse (R2) reads are paired together. Both files must be FASTQ 222 reverse (R2) reads are paired together. Both files must be FASTQ
190 format (``fastqsanger`` or ``fastqsanger.gz``). 223 format (``fastqsanger`` or ``fastqsanger.gz``).