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comparison qfilt.xml @ 1:8954237e00cf draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit acc9298b21e079245ea72c88fc95122bedb2fdff"
author iuc
date Sun, 18 Apr 2021 20:35:13 +0000
parents 94e7fce14cfd
children
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0:94e7fce14cfd 1:8954237e00cf
1 <?xml version="1.0"?> 1 <tool id="qfilt" version="1.0.0+galaxy1" name="qfilt" profile="20.01">
2 <tool id="qfilt" version="1.0.0" name="qfilt">
3 <description>filter sequencing data using simple heuristics</description> 2 <description>filter sequencing data using simple heuristics</description>
4 <requirements> 3 <requirements>
5 <requirement type="package" version="0.0.1">qfilt</requirement> 4 <requirement type="package" version="0.0.1">qfilt</requirement>
6 </requirements> 5 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
8 qfilt -o '$filtered_output' 7 qfilt -o '$filtered_output'
8 -f $output_format
9 #if str($options.advanced) == 'advanced': 9 #if str($options.advanced) == 'advanced':
10 -q $options.qscore 10 -q $options.qscore
11 -l $options.length 11 -l $options.length
12 $options.split 12 $options.split
13 #if $options.replace and $options.remove: 13 #if $options.replace and $options.remove:
18 #end if 18 #end if
19 #if $options.prefix: 19 #if $options.prefix:
20 -t $options.mismatch 20 -t $options.mismatch
21 -T '$options.prefix' 21 -T '$options.prefix'
22 #end if 22 #end if
23 -f $options.output_format
24 $options.tolerate_homopolymeric $options.tolerate_ambiguous 23 $options.tolerate_homopolymeric $options.tolerate_ambiguous
25 #end if 24 #end if
26 #if $input_data.format == 'fastq': 25 #if $input_data.format == 'fastq':
27 -Q '$input_data.fastq' 26 -Q
27 #if $input_data.fastq.ext.endswith('.gz')
28 <(zcat '$input_data.fastq')
29 #else
30 '$input_data.fastq'
31 #end if
28 #else: 32 #else:
29 -F '$input_data.fasta' 33 -F '$input_data.fasta'
30 '$input_data.qual' 34 '$input_data.qual'
31 #end if 35 #end if
32 ]]></command> 36 ]]></command>
35 <param name="format" type="select" label="Additional options"> 39 <param name="format" type="select" label="Additional options">
36 <option value="fastq">FASTQ</option> 40 <option value="fastq">FASTQ</option>
37 <option value="fastaq">FASTA+QUAL</option> 41 <option value="fastaq">FASTA+QUAL</option>
38 </param> 42 </param>
39 <when value="fastq"> 43 <when value="fastq">
40 <param name="fastq" argument="-Q" type="data" format="fastq" label="Input FASTA" help="FASTQ File" /> 44 <param name="fastq" argument="-Q" type="data" format="fastq,fastq.gz" label="Input FASTA" help="FASTQ File" />
41 </when> 45 </when>
42 <when value="fastaq"> 46 <when value="fastaq">
43 <param name="fasta" argument="-F" type="data" format="fasta" label="Input FASTA" help="FASTA File" /> 47 <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" /> 48 <param name="qual" argument="-F" type="data" format="qual" label="Input QUAL" help="FASTQ File" />
45 </when> 49 </when>
60 <param name="tolerate_ambiguous" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Tolerate Ambiguous" help="tolerate low q-score ambiguous nucleotides" /> 64 <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" /> 65 <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" /> 66 <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" /> 67 <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" /> 68 <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> 69 </when>
70 </conditional> 70 </conditional>
71 <param name="output_format" argument="-f" type="select" label="Format" help="output in FASTA or FASTQ format (default=FASTA)" >
72 <option value="FASTA">FASTA</option>
73 <option value="FASTQ">FASTQ</option>
74 </param>
71 </inputs> 75 </inputs>
72 <outputs> 76 <outputs>
73 <data format="fasta" name="filtered_output"> 77 <data format="fasta" name="filtered_output">
74 <change_format> 78 <change_format>
75 <when input="output_format" value="FASTQ" format="fastq" /> 79 <when input="output_format" value="FASTQ" format="fastq" />
76 </change_format> 80 </change_format>
77 </data> 81 </data>
78 </outputs> 82 </outputs>
79 <tests> 83 <tests>
80 <test> 84 <test>
81 <param name="fastq" value="qfilt-in1.fastq" /> 85 <param name="fastq" value="qfilt-in1.fastq" ftype="fastq" />
82 <output file="qfilt-out1.fa" ftype="fasta" name="filtered_output" /> 86 <output file="qfilt-out1.fa" ftype="fasta" name="filtered_output" />
83 </test> 87 </test>
84 <test> 88 <test>
85 <param name="format" value="fastq" /> 89 <param name="format" value="fastq" />
86 <param name="fastq" value="qfilt-in1.fastq" /> 90 <param name="fastq" value="qfilt-in1.fastq.gz" ftype="fastq.gz" />
87 <param name="advanced" value="advanced" /> 91 <param name="advanced" value="advanced" />
88 <param name="tolerate_homopolymeric" value="False" /> 92 <param name="tolerate_homopolymeric" value="False" />
89 <output file="qfilt-out2.fa" ftype="fasta" name="filtered_output" /> 93 <output file="qfilt-out2.fa" ftype="fasta" name="filtered_output" />
90 </test> 94 </test>
91 <test> 95 <test>
96
92 <param name="fasta" value="qfilt-in2.fa" /> 97 <param name="fasta" value="qfilt-in2.fa" />
93 <param name="qual" value="qfilt-in2.qual" /> 98 <param name="qual" value="qfilt-in2.qual" />
94 <param name="format" value="fastaq" /> 99 <param name="format" value="fastaq" />
95 <output file="qfilt-out3.fa" ftype="fasta" name="filtered_output" /> 100 <param name="output_format" value="FASTQ" />
101 <output file="qfilt-out3.fq" ftype="fastq" name="filtered_output" />
96 </test> 102 </test>
97 </tests> 103 </tests>
98 <help><![CDATA[ 104 <help><![CDATA[
99 qfilt 105 qfilt
100 ===== 106 =====