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comparison smudgeplot.xml @ 4:5e0825476fb7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 72ae2e05f35098c4cb6dd4f038bff07fd36917ed
author iuc
date Tue, 04 Apr 2023 17:23:19 +0000
parents 24e471d13fe9
children 5a0ddb4dc3a4
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3:24e471d13fe9 4:5e0825476fb7
1 <tool id="smudgeplot" name="Smudgeplot" version="@TOOL_VERSION@+galaxy+@VERSION_SUFFIX@" profile="21.05"> 1 <tool id="smudgeplot" name="Smudgeplot" version="@TOOL_VERSION@+galaxy+@VERSION_SUFFIX@" profile="21.05">
2 <description>inference of ploidy and heterozygosity structure using whole genome sequencing</description> 2 <description>inference of ploidy and heterozygosity structure using whole genome sequencing</description>
3 3
4 <macros> 4 <macros>
5 <token name="@TOOL_VERSION@">0.2.5</token> 5 <token name="@TOOL_VERSION@">0.2.5</token>
6 <token name="@VERSION_SUFFIX@">1</token> 6 <token name="@VERSION_SUFFIX@">2</token>
7 </macros> 7 </macros>
8 8
9 <xrefs> 9 <xrefs>
10 <xref type="bio.tools">smudgeplots</xref> 10 <xref type="bio.tools">smudgeplots</xref>
11 </xrefs> 11 </xrefs>
14 <requirement type="package" version="@TOOL_VERSION@">smudgeplot</requirement> 14 <requirement type="package" version="@TOOL_VERSION@">smudgeplot</requirement>
15 <requirement type="package" version="2.3.0">kmer-jellyfish</requirement> 15 <requirement type="package" version="2.3.0">kmer-jellyfish</requirement>
16 </requirements> 16 </requirements>
17 17
18 <command detect_errors="exit_code"><![CDATA[ 18 <command detect_errors="exit_code"><![CDATA[
19 set -o pipefail;
19 20
20 #if $file.input.input_select == 'reads' 21 #if $file.input.input_select == 'reads'
21 22
22 ## ~~~~~~~~~~~~~~~ Generate kmer-dump with presets ~~~~~~~~~~~~~~~~~~~~~ 23 ## ~~~~~~~~~~~~~~~ Generate kmer-dump with presets ~~~~~~~~~~~~~~~~~~~~~
23 24
24 ## Jellyfish kmer count 25 ## Jellyfish kmer count
25 ## --------------------------------------------------------------------- 26 ## ---------------------------------------------------------------------
26 27
27 #if $file.input.reads[0].is_of_type("fastqsanger.gz") or $file.input.reads[0].is_of_type("fasta.gz") 28 mkdir -p './files/' &&
28 gunzip -c 29 #if $file.input.reads[0].ext.endswith(".gz")
30 zcat
29 #for $f in $file.input.reads 31 #for $f in $file.input.reads
30 #if $f 32 '$f'
31 '$f'
32 #end if
33 | jellyfish count -m 21 -t 4 -s 1M -o 1_counts.jf -C /dev/stdin
34 #end for 33 #end for
35 34 | jellyfish count -m $file.input.mer_len -t \${GALAXY_SLOTS:-8} -s 1M -o 1_counts.jf -C /dev/stdin
36 #else 35 #else
37 jellyfish count -m 21 -t 4 -s 1M -o 1_counts.jf -C 36 jellyfish count -m $file.input.mer_len -t \${GALAXY_SLOTS:-8} -s 1M -o 1_counts.jf -C
38 #for $f in $file.input.reads 37 #for $f in $file.input.reads
39 #if $f 38 '$f'
40 '$f'
41 #end if
42 #end for 39 #end for
43 #end if 40 #end if
44 41
45 && jellyfish histo 1_counts.jf > 1_kmer_k21.hist 42 && jellyfish histo 1_counts.jf > 1_kmer_k21.hist
46 43
47 ## Calculate lower and upper kmer count cutoffs 44 ## Calculate lower and upper kmer count cutoffs
48 ## --------------------------------------------------------------------- 45 ## ---------------------------------------------------------------------
49 46
50 #if $file.input.lower_cutoff is not None: 47 #if $file.input.lower_cutoff:
51 && L=$file.input.lower_cutoff 48 && L=$file.input.lower_cutoff
52 #else 49 #else
53 && L=\$(smudgeplot.py cutoff 1_kmer_k21.hist L) 50 && L=\$(smudgeplot.py cutoff 1_kmer_k21.hist L)
54 #end if 51 #end if
55 52
56 #if $file.input.upper_cutoff is not None: 53 #if $file.input.upper_cutoff:
57 && U=$file.input.upper_cutoff 54 && U=$file.input.upper_cutoff
58 #else 55 #else
59 && U=\$(smudgeplot.py cutoff 1_kmer_k21.hist U) 56 && U=\$(smudgeplot.py cutoff 1_kmer_k21.hist U)
60 #end if 57 #end if
61 58
75 #end if 72 #end if
76 73
77 ## --------------------------------------------------------------------- 74 ## ---------------------------------------------------------------------
78 ## Plot 75 ## Plot
79 76
80 && smudgeplot.py plot 2_kmer_pairs_coverages.tsv -o my_genome 77 && smudgeplot.py plot $homozygous 2_kmer_pairs_coverages.tsv -o my_genome
81 78
82 ]]></command> 79 ]]></command>
83 80
84 <inputs> 81 <inputs>
85 <section name="file" title="File inputs" expanded="true"> 82 <section name="file" title="File inputs" expanded="true">
99 label="Sequencing reads" multiple="true" 96 label="Sequencing reads" multiple="true"
100 help="Sequencing reads corresponding to your genome. 97 help="Sequencing reads corresponding to your genome.
101 Don't worry about read pairing as it is not used in Kmer-counting. 98 Don't worry about read pairing as it is not used in Kmer-counting.
102 If selecting multiple datasets, please do not mix datatypes!" 99 If selecting multiple datasets, please do not mix datatypes!"
103 /> 100 />
101
102 <param argument="--mer-len"
103 type="integer"
104 min="1"
105 value="21"
106 label="K-mer size"
107 help="The size of k-mers should be large enough allowing the k-mer to map uniquely to the genome" />
108
104 109
105 <param 110 <param
106 name="lower_cutoff" 111 name="lower_cutoff"
112 min="1"
107 label="Lower kmer cutoff" 113 label="Lower kmer cutoff"
108 type="integer" 114 type="integer"
109 optional="true" 115 optional="true"
110 help="Optionally set a manual lower limit for filtering kmers with 116 help="Optionally set a manual lower limit for filtering kmers with
111 smudgeplot hetkmers. If no value is set, a cutoff will be 117 smudgeplot hetkmers. If no value is set, a cutoff will be
113 visualize your kmer histogram when choosing cutoff values." 119 visualize your kmer histogram when choosing cutoff values."
114 /> 120 />
115 121
116 <param 122 <param
117 name="upper_cutoff" 123 name="upper_cutoff"
124 min="1"
118 label="Upper kmer cutoff" 125 label="Upper kmer cutoff"
119 type="integer" 126 type="integer"
120 optional="true" 127 optional="true"
121 help="Optionally set a manual upper limit for filtering kmers with 128 help="Optionally set a manual upper limit for filtering kmers with
122 smudgeplot hetkmers. If no value is set, a cutoff will be 129 smudgeplot hetkmers. If no value is set, a cutoff will be
133 This enables control over kmer-counting parameters." 140 This enables control over kmer-counting parameters."
134 /> 141 />
135 </when> 142 </when>
136 </conditional> 143 </conditional>
137 </section> 144 </section>
145 <param argument="--homozygous" type="boolean" truevalue="--homozygous" falsevalue="" checked="false" label="Homozygous" help="Assume no heterozygosity in the genome - plotting a paralog structure." />
138 146
139 <param name="table_output" type="boolean" label="Output summary table"></param> 147 <param name="table_output" type="boolean" label="Output summary table"></param>
140 <param name="verbose_output" type="boolean" label="Output verbose summary"></param> 148 <param name="verbose_output" type="boolean" label="Output verbose summary"></param>
141 <param name="warnings_output" type="boolean" label="Output genome warnings"></param> 149 <param name="warnings_output" type="boolean" label="Output genome warnings"></param>
142 </inputs> 150 </inputs>
222 <test expect_num_outputs="2"> 230 <test expect_num_outputs="2">
223 <param name="input_select" value="dump"/> 231 <param name="input_select" value="dump"/>
224 <param name="dump" value="dump.jf" ftype="txt"/> 232 <param name="dump" value="dump.jf" ftype="txt"/>
225 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/> 233 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
226 </test> 234 </test>
235 <!-- Standard run without specifying cutoffs and compressed file -->
236 <test expect_num_outputs="2">
237 <param name="input_select" value="reads"/>
238 <param name="reads" value="test_reads_4.fasta.gz,test_reads_5.fasta.gz"/>
239 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot_02.png" compare="sim_size"/>
240 <assert_stdout>
241 <has_text text="Dump with cutoffs L=10, U=70" />
242 </assert_stdout>
243 </test>
227 </tests> 244 </tests>
228 245
229 <help><![CDATA[ 246 <help><![CDATA[
230 247
231 .. class:: infomark 248 .. class:: infomark