Mercurial > repos > iuc > meryl_trio_mode
comparison trio-mode.xml @ 0:c85aec7804a4 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
author | iuc |
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date | Thu, 25 Apr 2024 21:01:24 +0000 |
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-1:000000000000 | 0:c85aec7804a4 |
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1 <tool id="meryl_trio_mode" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@"> | |
2 <description>build hap-mers databases for trios</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="edam_ontology"/> | |
7 <xrefs> | |
8 <xref type="bio.tools">meryl</xref> | |
9 </xrefs> | |
10 <expand macro="requirements"/> | |
11 <version_command>meryl --version</version_command> | |
12 <command detect_errors="exit_code"><![CDATA[ | |
13 export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) && | |
14 export MERQURY=\$(dirname \$(command -v merqury.sh))/../share/merqury/ && | |
15 #if $options_kmer_size.kmer_size == 'estimate' | |
16 #from math import log | |
17 #set size=int(log(int($options_kmer_size.genome_size)*(1-float($options_kmer_size.collision_rate))/float($options_kmer_size.collision_rate))/log(4)) | |
18 #elif $options_kmer_size.kmer_size == 'provide' | |
19 #set size=$options_kmer_size.input_kmer_size | |
20 #end if | |
21 #for $i, $read in enumerate($paternal_reads): | |
22 mkdir 'paternal${i}.meryl' && | |
23 ln -s '$read' ./input_paternal_${i}.${read.ext} && | |
24 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_paternal_${i}.${read.ext} output 'paternal${i}.meryl' && | |
25 #end for | |
26 meryl union-sum paternal*.meryl output pat.meryl && | |
27 #for $i, $read in enumerate($maternal_reads): | |
28 mkdir 'maternal${i}.meryl' && | |
29 ln -s '$read' ./input_maternal_${i}.${read.ext} && | |
30 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_maternal_${i}.${read.ext} output 'maternal${i}.meryl' && | |
31 #end for | |
32 meryl union-sum maternal*.meryl output mat.meryl && | |
33 #for $i, $read in enumerate($child_reads): | |
34 mkdir 'child${i}.meryl' && | |
35 ln -s '$read' ./input_child_${i}.${read.ext} && | |
36 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_child_${i}.${read.ext} output 'child${i}.meryl' && | |
37 #end for | |
38 meryl union-sum child*.meryl output child.meryl && | |
39 meryl histogram child.meryl > read-db.hist && | |
40 tar -czf 'read-db.meryldb' child.meryl && | |
41 | |
42 ## mat specific kmers | |
43 meryl difference mat.meryl pat.meryl output mat.only.meryl && | |
44 meryl histogram mat.only.meryl > mat.only.hist && | |
45 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.only.hist > mat.only.ploidy && | |
46 VAR=`sed -n 2p mat.only.ploidy | awk '{print \$NF}'` && | |
47 meryl greater-than \$VAR output mat.only.filt.meryl mat.only.meryl && | |
48 | |
49 ## pat specific kmers | |
50 meryl difference pat.meryl mat.meryl output pat.only.meryl && | |
51 meryl histogram pat.only.meryl > pat.only.hist && | |
52 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.only.hist > pat.only.ploidy && | |
53 VAR=`sed -n 2p pat.only.ploidy | awk '{print \$NF}'` && | |
54 meryl greater-than \$VAR output pat.only.filt.meryl pat.only.meryl && | |
55 | |
56 ## shared kmers | |
57 meryl intersect output shared.meryl mat.meryl pat.meryl && | |
58 | |
59 ## mat hapmers | |
60 meryl intersect output mat.inherited.meryl child.meryl mat.only.filt.meryl && | |
61 meryl histogram mat.inherited.meryl > mat.inherited.hist && | |
62 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.inherited.hist > mat.inherited.ploidy && | |
63 VAR=`sed -n 2p mat.inherited.ploidy | awk '{print \$NF}'` && | |
64 meryl greater-than \$VAR output mat.hapmer.meryl mat.inherited.meryl && | |
65 tar -czf 'mat.meryldb' mat.hapmer.meryl && | |
66 | |
67 ## pat hapmers | |
68 meryl intersect output pat.inherited.meryl child.meryl pat.only.filt.meryl && | |
69 meryl histogram pat.inherited.meryl > pat.inherited.hist && | |
70 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.inherited.hist > pat.inherited.ploidy && | |
71 VAR=`sed -n 2p pat.inherited.ploidy | awk '{print \$NF}'` && | |
72 meryl greater-than \$VAR output pat.hapmer.meryl pat.inherited.meryl && | |
73 tar -czf 'pat.meryldb' pat.hapmer.meryl && | |
74 | |
75 echo 'K-mer size: ${size}' | |
76 ]]></command> | |
77 <inputs> | |
78 <param name="child_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly"/> | |
79 <param name="paternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly"/> | |
80 <param name="maternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly"/> | |
81 <conditional name="options_kmer_size"> | |
82 <param name="kmer_size" type="select" label="K-mer size selector"> | |
83 <option value="provide">Set a k-mer size</option> | |
84 <option value="estimate">Estimate the best k-mer size</option> | |
85 </param> | |
86 <when value="provide"> | |
87 <param name="input_kmer_size" type="integer" min="1" max="50" value="" label="K-mer size" help="For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G)."/> | |
88 </when> | |
89 <when value="estimate"> | |
90 <param name="genome_size" type="integer" min="1000" max="70000000000" value="1000" label="Genome size" help="Haploid genome size or diploid genome size, depending on what we evaluate. In bp. Only required if the k-mer size is not provided."/> | |
91 <param name="collision_rate" type="float" min="0.0001" max="0.01" value="0.001" label="Tolerable collision rate" help="Tolerable collision rate. By default is 0.001."/> | |
92 </when> | |
93 </conditional> | |
94 </inputs> | |
95 <outputs> | |
96 <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb" label="${tool.name} on ${on_string}: read-db.meryldb"/> | |
97 <data name="read_db_hist" format="tabular" from_work_dir="read-db.hist" label="${tool.name} on ${on_string}: read-db histogram"/> | |
98 <data name="pat_db" format="meryldb" from_work_dir="pat.meryldb" label="${tool.name} on ${on_string}: pat.meryldb"/> | |
99 <data name="pat_db_hist" format="tabular" from_work_dir="pat.inherited.hist" label="${tool.name} on ${on_string}: paternal inherited histogram"/> | |
100 <data name="mat_db" format="meryldb" from_work_dir="mat.meryldb" label="${tool.name} on ${on_string}: mat.meryldb"/> | |
101 <data name="mat_db_hist" format="tabular" from_work_dir="mat.inherited.hist" label="${tool.name} on ${on_string}: maternal inherited histogram"/> | |
102 </outputs> | |
103 <tests> | |
104 <test expect_num_outputs="6"> | |
105 <conditional name="options_kmer_size"> | |
106 <param name="kmer_size" value="provide"/> | |
107 <param name="input_kmer_size" value="21"/> | |
108 </conditional> | |
109 <param name="maternal_reads" value="maternal.fasta"/> | |
110 <param name="paternal_reads" value="paternal.fasta"/> | |
111 <param name="child_reads" value="child.fasta"/> | |
112 <output name="read_db" ftype="meryldb"> | |
113 <assert_contents> | |
114 <has_size value="3362942" delta="2000"/> | |
115 <expand macro="meryldb_archive_assumptions"/> | |
116 </assert_contents> | |
117 </output> | |
118 <output name="read_db_hist" file="output_23.read-db.hist"/> | |
119 <output name="pat_db" ftype="meryldb"> | |
120 <assert_contents> | |
121 <has_size value="120610" delta="400"/> | |
122 <expand macro="meryldb_archive_assumptions"/> | |
123 </assert_contents> | |
124 </output> | |
125 <output name="pat_db_hist" file="output_23.pat.hist"/> | |
126 <output name="mat_db" ftype="meryldb"> | |
127 <assert_contents> | |
128 <has_size value="67883" delta="300"/> | |
129 <expand macro="meryldb_archive_assumptions"/> | |
130 </assert_contents> | |
131 </output> | |
132 <output name="mat_db_hist" file="output_23.mat.hist"/> | |
133 </test> | |
134 </tests> | |
135 <help> | |
136 | |
137 .. class:: infomark | |
138 | |
139 **Purpose** | |
140 | |
141 Meryl is the k-mer counter. This tool builds hap-mer databases for trios, in accordance | |
142 with `merqury's recommended guidelines. <https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs#3-build-hap-mer-dbs-for-trios>`_ | |
143 | |
144 </help> | |
145 <expand macro="citations"/> | |
146 </tool> |