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comparison presto_maskprimers.xml @ 0:14e648d05cce draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
author iuc
date Wed, 30 May 2018 15:34:53 -0400
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children 61c1ae41a6bd
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1 <tool id="presto_maskprimers" name="pRESTO MaskPrimers" version="@PRESTO_VERSION@">
2 <description>Removes primers and annotates sequences with primer and barcode identifiers.</description>
3
4 <macros>
5 <import>presto_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9
10 <version_command>MaskPrimers.py --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 ln -s '$fastq_in' in.fastq &&
13 ln -s '$primers_in' primers.fasta &&
14 MaskPrimers.py '$cc.command'
15 --nproc "\${GALAXY_SLOTS:-1}"
16 -s in.fastq
17 -p primers.fasta
18 --mode '$mode'
19 --maxerror '$maxerror'
20 $revpr
21 $barcode
22
23 #if $cc.command == "align"
24 --maxlen '$cc.maxlen'
25 --gap '$cc.gap_open' '$cc.gap_extend'
26 $cc.skiprc
27 #end if
28
29 #if $cc.command == "score"
30 --start '$cc.start'
31 #end if
32
33 --outdir=.
34 --outname=tmp_mask
35 #if $capture_log
36 --log '$log_out'
37 #end if
38 ]]></command>
39 <inputs>
40 <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file"/>
41 <param argument="-p" name="primers_in" type="data" format="fasta" label="Primer FASTA file"/>
42 <param argument="--mode" type="select" value="mask" label="Mode" help="Specifies how identified primer sequences will be handled.">
43 <option value="cut">Remove primer and preceding sequence (cut)</option>
44 <option value="mask">Mask primer to Ns and remove preceding sequence (mask)</option>
45 <option value="trim">Leave primer intact and remove preceding sequence (trim)</option>
46 <option value="tag">Leave primer and preceding sequence intact (tag)</option>
47 </param>
48 <conditional name="cc">
49 <param name="command" type="select" label="Command">
50 <option value="align">Find primer matches using pairwise local alignment (align)</option>
51 <option value="score">Find primer matches by scoring primers at a fixed position (score)</option>
52 </param>
53 <when value="align">
54 <param argument="--maxlen" type="integer" value="50" label="Max Length" help="Maximum length of sequence window to search for primers."/>
55 <param argument="--skiprc" type="boolean" value="false" truevalue="--skiprc" falsevalue="" label="Skip Reverse Complement" help="Skip checking of reverse complement sequences."/>
56 <param name="gap_open" type="integer" value="1" label="Gap Open Penalty" help="Positive value of the gap open penalty."/>
57 <param name="gap_extend" type="integer" value="1" label="Gap Extension Penalty" help="Positive value of the gap extension penalty."/>
58 </when>
59 <when value="score">
60 <param argument="--start" type="integer" value="0" label="Start Position" help="The starting position of the primer."/>
61 </when>
62 </conditional>
63 <param argument="--revpr" type="boolean" value="false" truevalue="--revpr" falsevalue="" label="Reverse Match" help="Match the reverse complement of primer sequences against the ends of reads."/>
64 <param argument="--barcode" type="boolean" value="false" truevalue="--barcode" falsevalue="" label="Extract Barcodes (UMIs)" help="Capture the sequence preceding the primer as a UMI."/>
65 <param argument="--maxerror" type="float" value="0.2" label="Max Error Rate" help="Maximum allowable rate between read and primer sequence."/>
66 <expand macro="presto-log-param"/>
67 </inputs>
68
69 <outputs>
70 <data name="fastq_out" format="fastq" from_work_dir="tmp_mask_primers-pass.fastq"/>
71 <expand macro="presto-log-output"/>
72 </outputs>
73
74 <tests>
75 <test>
76 <param name="command" value="score"/>
77 <param name="fastq_in" value="presto_maskprimers_without_barcode_test_in.fastq"/>
78 <param name="start" value="0"/>
79 <param name="primers_in" value="read1_primers.fasta"/>
80 <param name="mode" value="cut"/>
81 <param name="maxerror" value="0.15"/>
82 <output name="fastq_out" file="presto_maskprimers_without_barcode_test_score_out.fastq" sort="true"/>
83 </test>
84 <test>
85 <param name="command" value="score"/>
86 <param name="fastq_in" value="presto_maskprimers_with_barcode_test_in.fastq"/>
87 <param name="start" value="17"/>
88 <param name="barcode" value="true"/>
89 <param name="primers_in" value="read2_primers.fasta"/>
90 <param name="mode" value="cut"/>
91 <param name="maxerror" value="0.15"/>
92 <output name="fastq_out" file="presto_maskprimers_with_barcode_test_score_out.fastq" sort="true"/>
93 </test>
94 <test>
95 <param name="command" value="align"/>
96 <param name="fastq_in" value="presto_maskprimers_without_barcode_test_in.fastq"/>
97 <param name="primers_in" value="read1_primers.fasta"/>
98 <param name="mode" value="cut"/>
99 <param name="maxerror" value="0.15"/>
100 <param name="maxlen" value="25"/>
101 <output name="fastq_out" file="presto_maskprimers_without_barcode_test_align_out.fastq" sort="true"/>
102 </test>
103 <test>
104 <param name="command" value="align"/>
105 <param name="fastq_in" value="presto_maskprimers_with_barcode_test_in.fastq"/>
106 <param name="barcode" value="true"/>
107 <param name="primers_in" value="read2_primers.fasta"/>
108 <param name="mode" value="cut"/>
109 <param name="maxerror" value="0.15"/>
110 <param name="maxlen" value="25"/>
111 <output name="fastq_out" file="presto_maskprimers_with_barcode_test_align_out.fastq" sort="true"/>
112 </test>
113 </tests>
114
115 <help><![CDATA[
116 Removes primers and annotates sequences with primer and barcode identifiers
117
118 See the `pRESTO online help <@PRESTO_URL_BASE@/MaskPrimers.html>`_ for more information.
119
120 @HELP_NOTE@
121 ]]></help>
122 <expand macro="citations" />
123 </tool>