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comparison qfilt.xml @ 0:94e7fce14cfd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit a91f1a9caaff225bea14afd9f7ede25769b02121
author iuc
date Mon, 18 Jun 2018 16:55:03 -0400
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1 <?xml version="1.0"?>
2 <tool id="qfilt" version="1.0.0" name="qfilt">
3 <description>filter sequencing data using simple heuristics</description>
4 <requirements>
5 <requirement type="package" version="0.0.1">qfilt</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 qfilt -o '$filtered_output'
9 #if str($options.advanced) == 'advanced':
10 -q $options.qscore
11 -l $options.length
12 $options.split
13 #if $options.replace and $options.remove:
14 -P '$options.replace'
15 -R '$options.remove'
16 #elif $options.mode:
17 -m $options.mode
18 #end if
19 #if $options.prefix:
20 -t $options.mismatch
21 -T '$options.prefix'
22 #end if
23 -f $options.output_format
24 $options.tolerate_homopolymeric $options.tolerate_ambiguous
25 #end if
26 #if $input_data.format == 'fastq':
27 -Q '$input_data.fastq'
28 #else:
29 -F '$input_data.fasta'
30 '$input_data.qual'
31 #end if
32 ]]></command>
33 <inputs>
34 <conditional name="input_data">
35 <param name="format" type="select" label="Additional options">
36 <option value="fastq">FASTQ</option>
37 <option value="fastaq">FASTA+QUAL</option>
38 </param>
39 <when value="fastq">
40 <param name="fastq" argument="-Q" type="data" format="fastq" label="Input FASTA" help="FASTQ File" />
41 </when>
42 <when value="fastaq">
43 <param name="fasta" argument="-F" type="data" format="fasta" label="Input FASTA" help="FASTA File" />
44 <param name="qual" argument="-F" type="data" format="qual" label="Input QUAL" help="FASTQ File" />
45 </when>
46 </conditional>
47
48 <conditional name="options">
49 <param name="advanced" type="select" label="Additional options">
50 <option value="defaults">Use defaults</option>
51 <option value="advanced">Specify additional parameters</option>
52 </param>
53 <when value="defaults"/>
54 <when value="advanced">
55 <param name="qscore" argument="-q" type="integer" value="20" label="QScore" help="minimum per-base quality score below which a read will be split or truncated" />
56 <param name="length" argument="-l" type="integer" value="50" label="Length" help="minimum retained fragment LENGTH" />
57 <param name="mode" argument="-m" type="integer" value="0" label="Mode" help="MODE is a 3-bitmask (an integer in [0-7], default=0)" />
58 <param name="split" argument="-s" type="boolean" truevalue="-s" falsevalue="" label="Split" help="when encountering a low q-score, split instead of truncate" />
59 <param name="tolerate_homopolymeric" argument="-p" type="boolean" truevalue="-p" falsevalue="" label="Tolerate Homopolymeric" help="tolerate low q-score homopolymeric regions" />
60 <param name="tolerate_ambiguous" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Tolerate Ambiguous" help="tolerate low q-score ambiguous nucleotides" />
61 <param name="replace" argument="-P" type="text" label="Replace" help="rather than splitting or truncating, replace low quality bases with CHAR this option OVERRIDES all -m mode options" />
62 <param name="remove" argument="-R" type="text" label="Remove" help="rather than splitting or truncating, remove reads which contain more than COUNT low quality bases this option only works in COMBINATION with the -P (punch) option" />
63 <param name="prefix" argument="-T" type="text" label="Prefix" help="if supplied, only reads with this PREFIX are retained, and the PREFIX is stripped from each contributing read" />
64 <param name="mismatch" argument="-t" type="integer" value="0" label="Mismatch" help="if PREFIX is supplied, prefix matching tolerates at most MISMATCH mismatches" />
65 <param name="output_format" argument="-f" type="select" label="Format" help="output in FASTA or FASTQ format (default=FASTA)" >
66 <option value="FASTA">FASTA</option>
67 <option value="FASTQ">FASTQ</option>
68 </param>
69 </when>
70 </conditional>
71 </inputs>
72 <outputs>
73 <data format="fasta" name="filtered_output">
74 <change_format>
75 <when input="output_format" value="FASTQ" format="fastq" />
76 </change_format>
77 </data>
78 </outputs>
79 <tests>
80 <test>
81 <param name="fastq" value="qfilt-in1.fastq" />
82 <output file="qfilt-out1.fa" ftype="fasta" name="filtered_output" />
83 </test>
84 <test>
85 <param name="format" value="fastq" />
86 <param name="fastq" value="qfilt-in1.fastq" />
87 <param name="advanced" value="advanced" />
88 <param name="tolerate_homopolymeric" value="False" />
89 <output file="qfilt-out2.fa" ftype="fasta" name="filtered_output" />
90 </test>
91 <test>
92 <param name="fasta" value="qfilt-in2.fa" />
93 <param name="qual" value="qfilt-in2.qual" />
94 <param name="format" value="fastaq" />
95 <output file="qfilt-out3.fa" ftype="fasta" name="filtered_output" />
96 </test>
97 </tests>
98 <help><![CDATA[
99 qfilt
100 =====
101
102 This simple program is meant to filter sequencing data with the option to:
103
104 - Remove or split reads with poor quality scores
105 - Retain only fragments from reads that are tagged with a given 5' sequence.
106
107 ^^^^^^^^
108
109 Example Output
110
111 >GM98SRO01B77KU rank=0000671 x=796.0 y=1996.0 length=58
112
113 CCACGCGTATCGATGTCGACTTTTTTTTCTTTTCTTACATAGTAG
114
115 >GM98SRO01BA3RP rank=0000953 x=419.5 y=1603.5 length=87
116
117 CTGATGCTGCACCAACTGTACTCCCTCGCGATA
118
119 >GM98SRO01E1BKW rank=0001233 x=1948.0 y=846.0 length=66
120
121 TACAGTTGGTGCAGCATCAGAAAAGTACGACATCGATACGCGTGGTCCTCGCGA
122
123 >GM98SRO01DVVNY rank=0001304 x=1476.0 y=636.5 length=84
124
125 ACGGCTGATGCTGCACCAACTGTACTCCCTCGCGATA
126
127 >GM98SRO01D6FIX rank=0001416 x=1596.0 y=1415.0 length=91
128
129 CGGCTGATGCTGCACCAACTGTACTCCCTCGCGATA
130 ]]></help>
131 <citations>
132 <citation type="bibtex">
133 @UNPUBLISHED{spond,
134 author = "Sergei Kosakovsky Pond",
135 title = "HyPhy: Hypothesis Testing using Phylogenies",
136 year = "2000",
137 note = "http://hyphy.org/",
138 url = "http://hyphy.org/"}
139 </citation>
140 </citations>
141 </tool>