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comparison presto_filterseq.xml @ 0:700a13dbe705 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 15:33:23 -0400
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children 4bfcc6c17fd8
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-1:000000000000 0:700a13dbe705
1 <tool id="presto_filterseq" name="pRESTO FilterSeq" version="@PRESTO_VERSION@">
2 <description>Filters and/or masks reads based on length, quality, missing bases and repeats.</description>
3
4 <macros>
5 <import>presto_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9
10 <version_command>FilterSeq.py --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 ln -s '$fastq_in' in.fastq &&
13 FilterSeq.py '$cc.command'
14 --nproc "\${GALAXY_SLOTS:-1}"
15 -s in.fastq
16 #if $varExists('cc.q')
17 -q '$cc.q'
18 #end if
19 #if $getVar('cc.inner', False)
20 --inner
21 #end if
22 #if $varExists('cc.win')
23 --win '$cc.win'
24 #end if
25 #if $getVar('cc.reverse', False)
26 --reverse
27 #end if
28 #if $varExists('cc.n')
29 -n '$cc.n'
30 #end if
31 --outdir=.
32 --outname=tmp_filter_seq
33 #if $capture_log
34 --log '$log_out'
35 #end if
36 &&
37 mv ./tmp_filter_seq_${cc.command}-pass.fastq $fastq_out
38 ]]></command>
39 <inputs>
40 <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file"/>
41 <conditional name="cc">
42 <param name="command" type="select" label="Command">
43 <option value="length">Filters reads by length (length)</option>
44 <option value="missing">Filters reads by N or gap character count (missing)</option>
45 <option value="repeats">Filters reads by consecutive nucleotide repeats (repeats)</option>
46 <option value="quality">Filters reads by quality score (quality)</option>
47 <option value="maskqual">Masks low quality positions (maskqual)</option>
48 <option value="trimqual">Trims sequences by quality score decay (trimqual)</option>
49 </param>
50 <when value="length">
51 <param argument="-n" type="integer" value="" label="Minimum Length" help="Discard reads shorter than this number of bases long."/>
52 </when>
53 <when value="missing">
54 <param argument="-n" type="integer" value="" label="Max Missing" help="Dicard reads with more than this many no-calls or gaps."/>
55 </when>
56 <when value="repeats">
57 <param argument="-n" type="integer" value="" label="Max Repeat Length" help="Discard reads with simple repeats of this length of longer."/>
58 </when>
59 <when value="quality">
60 <param argument="-q" type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/>
61 <param argument="--inner" type="boolean" value="false" label="End-Trim Ns" help="Exclude Ns at the ends of the reads from calculation."/>
62 </when>
63 <when value="maskqual">
64 <param argument="-q" type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/>
65 </when>
66 <when value="trimqual">
67 <param argument="-q" type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/>
68 <param argument="--win" type="integer" value="10" label="Window Size" help="Window size for moving average quality calculation."/>
69 <param argument="--reverse" type="boolean" value="false" label="Reverse" help="If true trim the start of the reads instead of the ends."/>
70 </when>
71 </conditional>
72 <expand macro="presto-log-param"/>
73 </inputs>
74
75 <outputs>
76 <data name="fastq_out" format="fastq"/>
77 <expand macro="presto-log-output"/>
78 </outputs>
79
80 <tests>
81 <test>
82 <param name="command" value="length"/>
83 <param name="n" value="299"/>
84 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
85 <output name="fastq_out" file="presto_filterseq_length_test_out.fastq" sort="true"/>
86 </test>
87 <test>
88 <param name="command" value="missing"/>
89 <param name="n" value="281"/>
90 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
91 <output name="fastq_out" file="presto_filterseq_missing_test_out.fastq" sort="true"/>
92 </test>
93 <test>
94 <param name="command" value="repeats"/>
95 <param name="n" value="8"/>
96 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
97 <output name="fastq_out" file="presto_filterseq_repeats_test_out.fastq" sort="true"/>
98 </test>
99 <test>
100 <param name="command" value="quality"/>
101 <param name="q" value="30"/>
102 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
103 <output name="fastq_out" file="presto_filterseq_quality_test_out.fastq" sort="true"/>
104 </test>
105 <test>
106 <param name="command" value="maskqual"/>
107 <param name="q" value="30"/>
108 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
109 <output name="fastq_out" file="presto_filterseq_maskqual_test_out.fastq" sort="true"/>
110 </test>
111 <test>
112 <param name="command" value="trimqual"/>
113 <param name="q" value="30"/>
114 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
115 <output name="fastq_out" file="presto_filterseq_trimqual_test_out.fastq" sort="true"/>
116 </test>
117 </tests>
118
119 <help><![CDATA[
120 Filters and/or masks reads based on length, quality, missing bases and repeats.
121
122 See the `pRESTO online help <@PRESTO_URL_BASE@/FilterSeq.html>`_ for more information.
123
124 @HELP_NOTE@
125 ]]></help>
126 <expand macro="citations" />
127 </tool>