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comparison mash_sketch.xml @ 2:91ee99b4f05a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
author iuc
date Sat, 24 Apr 2021 11:29:14 +0000
parents 68084b06ae83
children 43f9ca23c132
comparison
equal deleted inserted replaced
1:77289957d47b 2:91ee99b4f05a
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 mash sketch 11 mash sketch
12 -s '${sketch_size}' 12 -s '${sketch_size}'
13 -k '${kmer_size}' 13 -k '${kmer_size}'
14 -w '${prob_threshold}'
14 #if str ( $reads_assembly.reads_assembly_selector ) == "reads" 15 #if str ( $reads_assembly.reads_assembly_selector ) == "reads"
15 -m '${reads_assembly.minimum_kmer_copies}' 16 -m '${reads_assembly.minimum_kmer_copies}'
16 -r 17 -r
17 #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired" 18 #if $reads_assembly.target_coverage
18 '$reads_assembly.reads_input.reads_1' '$reads_assembly.reads_input.reads_2' 19 -c '${reads_assembly.target_coverage}'
19 #end if 20 #end if
20 #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection" 21 #if $reads_assembly.genome_size
21 '$reads_assembly.reads_input.reads.forward' '$reads_assembly.reads_input.reads.reverse' 22 -g '${reads_assembly.genome_size}'
22 #end if 23 #end if
23 #if str( $reads_assembly.reads_input.reads_input_selector ) == "single" 24 #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired"
24 '$reads_assembly.reads_input.reads' 25 '$reads_assembly.reads_input.reads_1' '$reads_assembly.reads_input.reads_2'
25 #end if 26 #end if
27 #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection"
28 '$reads_assembly.reads_input.reads.forward' '$reads_assembly.reads_input.reads.reverse'
29 #end if
30 #if str( $reads_assembly.reads_input.reads_input_selector ) == "single"
31 '$reads_assembly.reads_input.reads'
32 #end if
26 #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly" 33 #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly"
27 -p \${GALAXY_SLOTS:-1} 34 -p \${GALAXY_SLOTS:-1}
28 '${assembly}' 35 '${assembly}'
29 ${reads_assembly.individual_sequences} 36 ${reads_assembly.individual_sequences}
30 #end if 37 #end if
31 -o 'sketch' 38 -o 'sketch'
32 ]]></command> 39 ]]></command>
33 <inputs> 40 <inputs>
34 <conditional name="reads_assembly"> 41 <conditional name="reads_assembly">
53 <when value="paired_collection"> 60 <when value="paired_collection">
54 <param name="reads" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> 61 <param name="reads" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
55 </when> 62 </when>
56 </conditional> 63 </conditional>
57 <param type="integer" name="minimum_kmer_copies" argument="-m" value="1" min="1" max="1000" label="Minimum copies of each k-mer required to pass noise filter"/> 64 <param type="integer" name="minimum_kmer_copies" argument="-m" value="1" min="1" max="1000" label="Minimum copies of each k-mer required to pass noise filter"/>
65 <param type="integer" name="target_coverage" argument="-c" value="" min="0" max="500" optional="true" label="Target coverage" help="If specified, sketching will conclude if this coverage is reached before the end of the input file (estimated by average k-mer multiplicity)"/>
66 <param type="integer" name="genome_size" argument="-g" value="" min="1000" max="10 0000000000" optional="true" label="Genome size" help="If specified, will be used for p-value calculation instead of an estimated size from k-mer content"/>
58 </when> 67 </when>
59 <when value="assembly"> 68 <when value="assembly">
60 <param name="assembly" type="data" format="fasta,fasta.gz" label="Assembly"/> 69 <param name="assembly" type="data" format="fasta,fasta.gz" label="Assembly"/>
61 <param type="boolean" name="individual_sequences" truevalue="-i" falsevalue="" label="Sketch individual Sequences"/> 70 <param type="boolean" name="individual_sequences" truevalue="-i" falsevalue="" label="Sketch individual Sequences" help="Sketch individual sequences, rather than whole files, e.g. for multi-fastas of single-chromosome genomes or pair-wise gene comparisons"/>
62 </when> 71 </when>
63 </conditional> 72 </conditional>
64 <param type="integer" name="sketch_size" argument="-s" value="1000" min="10" max="1000000" label="Sketch size" /> 73 <param type="integer" name="sketch_size" argument="-s" value="1000" min="10" max="1000000" label="Sketch size" help="Each sketch will have at most this many non-redundant min-hashes"/>
65 <param type="integer" name="kmer_size" argument="-k" value="21" min="1" max="32" label="kmer size" /> 74 <param type="integer" name="kmer_size" argument="-k" value="21" min="1" max="32" label="kmer size" />
75 <param type="float" name="prob_threshold" argument="-w" value="0.01" min="0" max="1" label="Probability threshold for warning about low k-mer size" />
66 </inputs> 76 </inputs>
67 <outputs> 77 <outputs>
68 <data name="sketch" format="msh" from_work_dir="sketch.msh"/> 78 <data name="sketch" format="msh" from_work_dir="sketch.msh"/>
69 </outputs> 79 </outputs>
70 <tests> 80 <tests>
71 <test> 81 <test>
72 <param name="reads_assembly_selector" value="reads" /> 82 <conditional name="reads_assembly">
73 <param name="reads_input_selector" value="single"/> 83 <param name="reads_assembly_selector" value="reads"/>
74 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/> 84 <conditional name="reads_input">
75 <output name="sketch" file="ERR024951_seqtk_sample_1000_1.sketch.msh" compare="sim_size" /> 85 <param name="reads_input_selector" value="single"/>
86 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
87 </conditional>
88 </conditional>
89 <output name="sketch" file="test_01_mash_sketch.msh" compare="sim_size" />
76 </test> 90 </test>
77 <test> 91 <test>
78 <param name="reads_assembly_selector" value="assembly" /> 92 <conditional name="reads_assembly">
79 <param name="assembly" value="test_assembly.fasta"/> 93 <param name="reads_assembly_selector" value="reads"/>
80 <output name="sketch" file="test_assembly.sketch.msh" compare="sim_size" /> 94 <conditional name="reads_input">
95 <param name="reads_input_selector" value="single"/>
96 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
97 <param name="minimum_kmer_copies" value="10"/>
98 </conditional>
99 </conditional>
100 <output name="sketch" file="test_02_mash_sketch.msh" compare="sim_size" />
101 </test>
102 <test>
103 <conditional name="reads_assembly">
104 <param name="reads_assembly_selector" value="reads"/>
105 <conditional name="reads_input">
106 <param name="reads_input_selector" value="single"/>
107 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
108 <param name="target_coverage" value="1"/>
109 </conditional>
110 </conditional>
111 <output name="sketch" file="test_03_mash_sketch.msh" compare="sim_size" />
112 </test>
113 <test>
114 <conditional name="reads_assembly">
115 <param name="reads_assembly_selector" value="reads"/>
116 <conditional name="reads_input">
117 <param name="reads_input_selector" value="single"/>
118 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
119 <param name="genome_size" value="1000"/>
120 </conditional>
121 </conditional>
122 <output name="sketch" file="test_04_mash_sketch.msh" compare="sim_size" />
123 </test>
124 <test>
125 <conditional name="reads_assembly">
126 <param name="reads_assembly_selector" value="reads"/>
127 <conditional name="reads_input">
128 <param name="reads_input_selector" value="single"/>
129 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
130 </conditional>
131 </conditional>
132 <param name="sketch_size" value="500"/>
133 <output name="sketch" file="test_05_mash_sketch.msh" compare="sim_size" />
134 </test>
135 <test>
136 <conditional name="reads_assembly">
137 <param name="reads_assembly_selector" value="reads"/>
138 <conditional name="reads_input">
139 <param name="reads_input_selector" value="single"/>
140 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
141 </conditional>
142 </conditional>
143 <param name="kmer_size" value="17"/>
144 <output name="sketch" file="test_06_mash_sketch.msh" compare="sim_size" />
145 </test>
146 <test>
147 <conditional name="reads_assembly">
148 <param name="reads_assembly_selector" value="reads"/>
149 <conditional name="reads_input">
150 <param name="reads_input_selector" value="single"/>
151 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
152 </conditional>
153 </conditional>
154 <param name="prob_threshold" value="0.1"/>
155 <output name="sketch" file="test_06_mash_sketch.msh" compare="sim_size" />
156 </test>
157 <test>
158 <conditional name="reads_assembly">
159 <param name="reads_assembly_selector" value="assembly"/>
160 <param name="assembly" value="test_assembly.fasta"/>
161 </conditional>
162 <output name="sketch" file="test_07_mash_sketch.msh" compare="sim_size" />
81 </test> 163 </test>
82 </tests> 164 </tests>
83 <help><![CDATA[ 165 <help><![CDATA[
84 166
85 **What it does** 167 **What it does**