Mercurial > repos > iuc > presto_buildconsensus

comparison presto_buildconsensus.xml @ 0:7c7df98db5a9 draft

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/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
author iuc
date Wed, 30 May 2018 15:37:30 -0400
parents
children 379f74eae0ab
comparison
equal deleted inserted replaced
-1:000000000000 0:7c7df98db5a9
1 <tool id="presto_buildconsensus" name="pRESTO BuildConsensus" version="@PRESTO_VERSION@">
2 <description>Builds a consensus sequence for each set of input sequences</description>
3
4 <macros>
5 <import>presto_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9
10 <version_command>BuildConsensus.py --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 ln -s '$fastq_in' in.fastq &&
13 BuildConsensus.py
14 --nproc "\${GALAXY_SLOTS:-1}"
15 -s in.fastq
16 -n '$n'
17 --bf '$bf'
18 -q '$q'
19 --freq '$freq'
20 #if $maxgap
21 --maxgap '$maxgap'
22 #end if
23 #if $pf
24 --pf '$pf'
25 #end if
26 #if $prcons
27 --prcons '$prcons'
28 #end if
29 #if $cf
30 --cf $cf
31 #end if
32 #if $act
33 --act $act
34 #end if
35 $dep
36
37 #if $filtering.filter == "diversity"
38 --maxdiv '$filtering.maxdiv'
39 #end if
40 #if $filtering.filter == "error"
41 --maxerror '$filtering.maxerror'
42 #end if
43
44 --outname=tmp
45 #if $capture_log
46 --log '$log_out'
47 #end if
48 ]]></command>
49
50 <inputs>
51 <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file" help="FASTQ file of sequences with barcodes/UMIs in an annotation."/>
52 <param argument="-n" type="integer" value="1" label="Min Count" help="Minimum number of squences to form a valid consensus."/>
53 <param argument="--bf" type="text" value="BARCODE" label="Barcode Field" help="Name of the annotation field which contains the barcode/UMI sequence."/>
54 <param argument="-q" type="integer" value="0" label="Min Quality" help="Minimum quality under which an ambiguous character is assigned to a consensus base."/>
55 <param argument="--freq" type="float" value="0.6" label="Min Frequency" help="At a given position the fraction of basecalls required to agree to output an unambiguous base."/>
56 <param argument="--maxgap" type="float" value="" optional="true" label="Max Gap Fraction" help="Positions with greater than this fraction of gaps are deleted from the consensus."/>
57 <param argument="--pf" type="text" value="" optional="true" label="Primer Field" help="Name of the annotation field which contains the primer sequence (often PRIMER)."/>
58 <param argument="--prcons" type="float" value="" optional="true" label="Primer Consensus Frequency" help="Specify to define a minimum primer frequency required to assign a consensus primer, and filter out sequences with minority primers from the consensus building step."/>
59 <param argument="--cf" type="text" value="" optional="true" label="Copy Fields" help="Zero or more space-separated annotations to copy from input sequences to consensus sequences.">
60 <expand macro="text-regex-validator"/>
61 </param>
62 <param argument="--act" type="text" value="" optional="true" label="Copy Actions" help="Space-separated list of actions to take on copied annotations. Must be of same length as Copy Fields. Options are: min,max,sum,set,majority.">
63 <expand macro="text-regex-validator"/>
64 </param>
65 <param argument="--dep" type="boolean" value="false" truevalue="--dep" falsevalue="" label="Dependent Model" help="Specify to calculate consensus quality with a non-independence assumption."/>
66 <expand macro="presto-log-param"/>
67
68 <conditional name="filtering">
69 <param name="filter" type="select" label="Filtering Strategy">
70 <option value="none">No filtering of consensus reads.</option>
71 <option value="diversity">Filter by diversity (average pairwise error rate of input reads).</option>
72 <option value="error">Filters by error rate of input reads vs. consensus.</option>
73 </param>
74 <when value="diversity">
75 <param argument="--maxdiv" type="float" value="" label="Max Diversity" help="Remove consensus reads with average pairwise error between input reads above this cutoff [0-1]."/>
76 </when>
77 <when value="error">
78 <param argument="--maxerror" type="float" value="" label="Max Error" help="Remove consensus reads with average error vs. input reads above this cutoff [0-1]."/>
79 </when>
80 <when value="none"/>
81 </conditional>
82 </inputs>
83
84 <outputs>
85 <data name="fastq_out" format="fastq" from_work_dir="tmp_consensus-pass.fastq"/>
86 <expand macro="presto-log-output"/>
87 </outputs>
88
89 <tests>
90 <test>
91 <param name="fastq_in" value="presto_buildconsensus_test_input.fastq"/>
92 <param name="n" value="2"/>
93 <param name="pf" value="PRIMER"/>
94 <param name="maxgap" value="0.5"/>
95 <param name="prcons" value="0.6"/>
96 <param name="filter" value="error"/>
97 <param name="maxerror" value="0.1"/>
98 <output name="fastq_out" file="presto_buildconsensus_test_maxerror_output.fastq" sort="true"/>
99 </test>
100 <test>
101 <param name="fastq_in" value="presto_buildconsensus_test_input.fastq"/>
102 <param name="n" value="2"/>
103 <param name="pf" value="PRIMER"/>
104 <param name="maxgap" value="0.5"/>
105 <param name="prcons" value="0.6"/>
106 <param name="filter" value="diversity"/>
107 <param name="maxdiv" value="0.05"/>
108 <output name="fastq_out" file="presto_buildconsensus_test_maxdiv_output.fastq" sort="true"/>
109 </test>
110 </tests>
111
112 <help><![CDATA[
113 Builds a consensus sequence for each set of input sequences.
114
115 See the `pRESTO online help <@PRESTO_URL_BASE@/BuildConsensus.html>`_ for more information.
116
117 @HELP_NOTE@
118 ]]></help>
119 <expand macro="citations" />
120 </tool>