Mercurial > repos > iuc > nonpareil

annotate nonpareil.xml @ 2:cef64c36c89e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 0b535bf15f4bb0110f599c1af9b1dc1c66302899
author iuc
date Tue, 12 Mar 2024 08:50:50 +0000
parents 45210df786b9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
45210df786b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 46f7675fa6e17042965d1a8e5e368ed1c482f08c
iuc
parents: 0
diff changeset
1 <tool id="nonpareil" name="Nonpareil" version="@TOOL_VERSION@.1" profile="21.01">
0
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
2 <description>to estimate average coverage and generate Nonpareil curves</description>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
3 <macros>
2
cef64c36c89e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 0b535bf15f4bb0110f599c1af9b1dc1c66302899
iuc
parents: 1
diff changeset
4 <import>macros.xml</import>
0
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
5 </macros>
2
cef64c36c89e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 0b535bf15f4bb0110f599c1af9b1dc1c66302899
iuc
parents: 1
diff changeset
6 <expand macro="xrefs"/>
cef64c36c89e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 0b535bf15f4bb0110f599c1af9b1dc1c66302899
iuc
parents: 1
diff changeset
7 <expand macro="requirements"/>
0
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
8 <version_command>nonpareil -V</version_command>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
9 <command detect_errors="exit_code">
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
10 <![CDATA[
1
45210df786b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 46f7675fa6e17042965d1a8e5e368ed1c482f08c
iuc
parents: 0
diff changeset
11 ln -s '$input' input &&
45210df786b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 46f7675fa6e17042965d1a8e5e368ed1c482f08c
iuc
parents: 0
diff changeset
12
0
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
13 nonpareil
1
45210df786b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 46f7675fa6e17042965d1a8e5e368ed1c482f08c
iuc
parents: 0
diff changeset
14 -s input
0
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
15 -T '$algo'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
16 #if $input.is_of_type("fasta")
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
17 -f 'fasta'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
18 #else if $input.is_of_type("fastq")
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
19 -f 'fastq'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
20 #end if
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
21 -d '$subsampling'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
22 -n '$subsample_per_point'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
23 -L '$min_overlapping'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
24 -X '$max_query_reads'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
25 -R \${NONPAREIL_MAX_MEMORY:-1024}
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
26 -t \${GALAXY_SLOTS:-2}
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
27 -b output
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
28 -a '$all_data_output'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
29 -C '$mating_vector_output'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
30 #if $log_test
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
31 -l '$log'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
32 #end if
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
33 -o '$summary'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
34 $use_portion_in_output
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
35 -m '$sampling.min_sampling_portion'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
36 -M '$sampling.max_sampling_portion'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
37 -i '$sampling.sampling_portion_interval'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
38 $mating.use_rev_comp
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
39 $mating.n_as_mismatches
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
40 #if str($mating.sim_thres) != ''
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
41 -S '$mating.sim_thres'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
42 #end if
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
43 -k '$mating.kmer_size'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
44 #if str($mating.proba) != ''
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
45 -x '$mating.proba'
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
46 #end if
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
47 -r '$seed'
1
45210df786b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 46f7675fa6e17042965d1a8e5e368ed1c482f08c
iuc
parents: 0
diff changeset
48 && echo $log_test
0
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
49 ]]></command>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
50 <inputs>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
51 <param name="input" type="data" format="fastq,fasta" label="Input sequences" help="FastQ format is recommended for kmer algorithm and Fasta for the alignment" argument="-s"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
52 <param name="algo" type="select" label="Nonpareil algorithm?" argument="-T">
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
53 <option value="kmer">Kmer</option>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
54 <option value="alignment">Alignment</option>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
55 </param>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
56 <param name="subsampling" type="float" value="0.7" min="0" label="Factor for subsampling" help="Subsample iteratively applying this factor to the number of reads, resulting in logarithmic subsampling. Use 0 to fall back to linear sampling, control" argument="-d"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
57 <param name="subsample_per_point" type="integer" value="1024" min="0" label="Number of sub-samples to generate per point" help="If it is not a multiple of the number of threads, it is rounded to the next (upper) multiple" argument="-n"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
58 <param name="min_overlapping" type="integer" value="50" min="0" max="100" label="Minimum overlapping percentage of the aligned region on the largest sequence" help="The similarity is evaluated for the aligned region only" argument="-L"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
59 <param name="max_query_reads" type="integer" value="1000" min="0" label="Maximum number of reads to use as query" argument="-X"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
60 <param name="use_portion_in_output" type="boolean" truevalue="-F" falsevalue="" checked="false" label="Report the sampled portions as a fraction of the library instead of the number of reads?" argument="-F"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
61 <section name="sampling" title="Sampling" expanded="False">
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
62 <param name="min_sampling_portion" type="float" value="0" min="0" label="Minimum value of sampling portion" argument="-m"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
63 <param name="max_sampling_portion" type="float" value="1" min="0" label="Maximum value of sampling portion" argument="-M"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
64 <param name="sampling_portion_interval" type="float" value="0.01" min="0" label="Interval between sampling portions" argument="-i"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
65 </section>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
66 <section name="mating" title="Mating" expanded="False">
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
67 <param name="use_rev_comp" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Do not use reverse-complement?" help="This is useful for single stranded sequences data" argument="-c"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
68 <param name="n_as_mismatches" type="boolean" truevalue="-N" falsevalue="" checked="false" label="Treat Ns as mismatches?" help="By default, Ns (unknown nucleotides) match any nucleotide" argument="-N"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
69 <param name="sim_thres" type="float" optional="true" label="Similarity threshold" help="Reducing this option will increase sensitivity while increasing running time" argument="-S"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
70 <param name="kmer_size" type="integer" value="24" min="0" label="Kmer size" help="You can increase kmer size to increase sensitivity" argument="-k"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
71 <param name="proba" type="float" optional="true" label="Probability of taking a sequence into account as query for the construction of the curve" help="Higher values reduce accuracy but increase speed. If set, it overides the maximum number of reads to use as query" argument="-x"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
72 </section>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
73 <param name="seed" type="integer" value="1000" min="0" label="Random generator seed?" argument="-r"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
74 <param name="log_test" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output log file?"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
75 </inputs>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
76 <outputs>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
77 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: Redundancy summary">
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
78 <actions>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
79 <action name="column_names" type="metadata" default="sequencing_effort,average_redundancy,std,quartile_1,median,quartile_3" />
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
80 </actions>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
81 </data>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
82 <data format="tabular" name="all_data_output" label="${tool.name} on ${on_string}: Redundancy values for all the results">
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
83 <actions>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
84 <action name="column_names" type="metadata" default="sequencing_effort,replicate_id estimated_redundancy" />
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
85 </actions>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
86 </data>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
87 <data format="txt" name="log" label="${tool.name} on ${on_string}: Log">
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
88 <filter>log_test</filter>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
89 </data>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
90 <data format="tabular" name="mating_vector_output" label="${tool.name} on ${on_string}: Mates distribution"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
91 </outputs>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
92 <tests>
1
45210df786b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 46f7675fa6e17042965d1a8e5e368ed1c482f08c
iuc
parents: 0
diff changeset
93 <test expect_num_outputs="4">
0
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
94 <param name="input" value="test.fasta"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
95 <param name="algo" value="alignment"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
96 <param name="subsampling" value="0.7"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
97 <param name="subsample_per_point" value="1024"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
98 <param name="min_overlapping" value="50"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
99 <param name="max_query_reads" value="1000"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
100 <param name="use_portion_in_output" value="" />
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
101 <section name="sampling">
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
102 <param name="min_sampling_portion" value="0"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
103 <param name="max_sampling_portion" value="1"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
104 <param name="sampling_portion_interval" value="0.01"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
105 </section>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
106 <section name="mating">
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
107 <param name="use_rev_comp" value=""/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
108 <param name="n_as_mismatches" value=""/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
109 <param name="kmer_size" value="24"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
110 </section>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
111 <param name="seed" value="1000"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
112 <param name="log_test" value="true"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
113 <output name="all_data_output" value="test1-all_data_output" compare="sim_size" delta="0"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
114 <output name="log">
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
115 <assert_contents>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
116 <has_text text="Counting sequences" />
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
117 <has_text text="Evaluating consistency" />
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
118 <has_text text="Everything seems correct" />
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
119 </assert_contents>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
120 </output>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
121 <output name="summary" value="test1-summary" compare="sim_size" delta="0"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
122 <output name="mating_vector_output" value="test1-mating_vector_output" compare="sim_size" delta="0"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
123 </test>
1
45210df786b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 46f7675fa6e17042965d1a8e5e368ed1c482f08c
iuc
parents: 0
diff changeset
124 <test expect_num_outputs="3">
0
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
125 <param name="input" value="test.fastq"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
126 <param name="algo" value="kmer"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
127 <param name="subsampling" value="0.7"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
128 <param name="subsample_per_point" value="1024"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
129 <param name="min_overlapping" value="50"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
130 <param name="max_query_reads" value="10"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
131 <param name="use_portion_in_output" value="" />
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
132 <section name="sampling">
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
133 <param name="min_sampling_portion" value="0"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
134 <param name="max_sampling_portion" value="1"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
135 <param name="sampling_portion_interval" value="0.01"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
136 </section>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
137 <section name="mating">
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
138 <param name="use_rev_comp" value=""/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
139 <param name="n_as_mismatches" value=""/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
140 <param name="kmer_size" value="24"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
141 </section>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
142 <param name="seed" value="1000"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
143 <param name="log_test" value="false"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
144 <output name="all_data_output" value="test2-all_data_output" compare="sim_size" delta="0"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
145 <output name="summary" value="test2-summary" compare="sim_size" delta="0"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
146 <output name="mating_vector_output" value="test2-mating_vector_output" compare="sim_size" delta="5"/>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
147 </test>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
148 </tests>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
149 <help><![CDATA[
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
150 Nonpareil uses the redundancy of the reads in metagenomic datasets to estimate the average coverage and predict the amount of sequences that will be required to achieve "nearly complete coverage".
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
151
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
152 Nonpareil outputs three files and one optional log file:
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
153
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
154 - Redundancy summary is a tab-delimited file with six columns. The first column indicates the sequencing effort (in number of reads), and the remaining columns indicate the summary of the distribution of redundancy (from the replicates, 1,024 by default) at the given sequencing effort. These five columns are: average redundancy, standard deviation, quartile 1, median (quartile 2), and quartile 3.
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
155 - Redundancy values is a tab-delimited file with three columns. Similar to the redundancy summary file, it contains information about the redundancy at each sequencing effort, but it provides ALL the results from the replicates, not only the summary at each point. The first column indicates the sequencing effort (as a fraction of the dataset), the second column indicates the ID of the replicate (a number used only to introduce some controlled noise in plots), and the third column indicates the estimated redundancy value.
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
156 - Mates distribution is a raw list with the number of reads in the dataset matching a query read. A set of query reads is randomly drawn by Nonpareil (1,000 by default), and compared against all reads in the dataset. Each line on this file corresponds to a query read (the order is not important). We have seen certain correspondance between these numbers and the distribution of abundances in the community (compared, for example, as rank-abundance plots), but this file is provided only for quality-control purposes and comparisons with other tools.
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
157 - Log is a verbose log of internal Nonpareil processing. The number to the left (inside squared brackets) indicate the CPU time (in minutes). This file also provide quality assessment of the Nonpareil run (automated consistency evaluation). Ideally, the last line should read "Everything seems correct". Otherwise, it suggests alternative parameters that may improve the estimation.
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
158
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
159 For more details about the tool, please check: http://nonpareil.readthedocs.io/en/latest/index.html
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
160 ]]></help>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
161 <citations>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
162 <citation type="doi">10.1093/bioinformatics/btt584</citation>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
163 </citations>
280386b252a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit dba1b944c94d0adbfa2e8ee8068ee5b80e4ca583
iuc
parents:
diff changeset
164 </tool>