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comparison yac.xml @ 3:94d67b195acd draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
author artbio
date Mon, 21 Jan 2019 18:46:04 -0500
parents da08e89abd18
children f7947c5a18b8
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2:da08e89abd18 3:94d67b195acd
1 <tool id="yac" name="Clip adapter" version="2.1.1"> 1 <tool id="yac" name="Clip adapter" version="2.2.0">
2 <description /> 2 <description />
3 <command detect_errors="exit_code"><![CDATA[ 3 <command detect_errors="exit_code"><![CDATA[
4 python $__tool_directory__/yac.py 4 python $__tool_directory__/yac.py
5 --input $input 5 --input $input
6 --output $output 6 --output 'clip.tmp'
7 --output_format "$out_format" 7 --output_format
8 #if $out_format == 'fasta' or $out_format == 'fastagz':
9 'fasta'
10 #else
11 'fastq'
12 #end if
8 --adapter_to_clip $clip_source.clip_sequence 13 --adapter_to_clip $clip_source.clip_sequence
9 --min $min 14 --min $min
10 --max $max 15 --max $max
11 --Nmode $Nmode 16 --Nmode $Nmode &&
17 #if ($out_format == 'fastagz') or ($out_format == 'fastqgz'):
18 gzip -c 'clip.tmp' > $output
19 #else
20 mv clip.tmp $output
21 #end if
22
12 ]]></command> 23 ]]></command>
13 <inputs> 24 <inputs>
14 <param format="fastq" label="Source file" name="input" type="data" /> 25 <param format="fasta,fastq" label="Source file" name="input" type="data" />
15 <param label="min size" name="min" size="4" type="integer" value="15" /> 26 <param label="min size" name="min" size="4" type="integer" value="15" />
16 <param label="max size" name="max" size="4" type="integer" value="36" /> 27 <param label="max size" name="max" size="4" type="integer" value="36" />
17 <param label="Select output format" name="out_format" type="select"> 28 <param label="Select output format" name="out_format" type="select"
18 <option selected="true" value="fasta">Fasta format</option> 29 help="be careful not to select a fastq format for your output if your input has a fasta format">
19 <option value="fastq">Fastq (Sanger) format</option> 30 <option value="fasta">Fasta</option>
31 <option value="fastq" selected="true" >Fastq (Sanger)</option>
32 <option value="fastagz">gzipped Fasta</option>
33 <option value="fastqgz">gzipped Fastq (Sanger)</option>
20 </param> 34 </param>
21 <param label="Accept reads containing N?" name="Nmode" type="select"> 35 <param label="Accept reads containing N?" name="Nmode" type="select">
22 <option selected="True" value="accept">accept</option> 36 <option selected="True" value="accept">accept</option>
23 <option value="reject">reject</option> 37 <option value="reject">reject</option>
24 </param> 38 </param>
39 <param label="Enter your Sequence" name="clip_sequence" size="35" type="text" value="GAATCC" /> 53 <param label="Enter your Sequence" name="clip_sequence" size="35" type="text" value="GAATCC" />
40 </when> 54 </when>
41 </conditional> 55 </conditional>
42 </inputs> 56 </inputs>
43 <outputs> 57 <outputs>
44 <data format_source="input" metadata_source="input" name="output" label="Clipping of ${input.name}"> 58 <data format_source="input" metadata_source="input" name="output" label="Clipped ${input.name}-then-${out_format}">
45 <change_format> 59 <change_format>
46 <when input="out_format" value="fasta" format="fasta" /> 60 <when input="out_format" value="fasta" format="fasta" />
61 <when input="out_format" value="fastq" format="fastqsanger" />
62 <when input="out_format" value="fastagz" format="fasta.gz" />
63 <when input="out_format" value="fastqgz" format="fastqsanger.gz" />
47 </change_format> 64 </change_format>
48 </data> 65 </data>
49 </outputs> 66 </outputs>
50 <tests> 67 <tests>
51 <test> 68 <test>
53 <param name="min" value="18" /> 70 <param name="min" value="18" />
54 <param name="max" value="29" /> 71 <param name="max" value="29" />
55 <param name="clip_source_list" value="prebuilt" /> 72 <param name="clip_source_list" value="prebuilt" />
56 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" /> 73 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
57 <param name="Nmode" value="accept" /> 74 <param name="Nmode" value="accept" />
58 <output file="yac.out" name="output" /> 75 <param name="out_format" value="fastq" />
76 <output file="out.fastqsanger" name="output" />
59 </test> 77 </test>
60 <test> 78 <test>
61 <param ftype="fastqsanger" name="input" value="yac.fastq" /> 79 <param ftype="fastqsanger" name="input" value="yac.fastq" />
62 <param name="min" value="18" /> 80 <param name="min" value="18" />
63 <param name="max" value="29" /> 81 <param name="max" value="29" />
64 <param name="clip_source_list" value="prebuilt" /> 82 <param name="clip_source_list" value="prebuilt" />
65 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" /> 83 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
66 <param name="Nmode" value="accept" /> 84 <param name="Nmode" value="accept" />
67 <param name="out_format" value="fastq" /> 85 <param name="out_format" value="fasta" />
68 <output file="yac_fastq.out" name="output" /> 86 <output file="out.fasta" name="output" />
87 </test>
88 <test>
89 <param ftype="fastqsanger.gz" name="input" value="yac.fastqsanger.gz" />
90 <param name="min" value="18" />
91 <param name="max" value="29" />
92 <param name="clip_source_list" value="prebuilt" />
93 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
94 <param name="Nmode" value="accept" />
95 <param name="out_format" value="fastqgz" />
96 <output file="out.fastqsanger.gz" name="output" decompress="True" />
97 </test>
98 <test>
99 <param ftype="fastqsanger.gz" name="input" value="yac.fastqsanger.gz" />
100 <param name="min" value="18" />
101 <param name="max" value="29" />
102 <param name="clip_source_list" value="prebuilt" />
103 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
104 <param name="Nmode" value="accept" />
105 <param name="out_format" value="fastagz" />
106 <output file="out.fasta.gz" name="output" decompress="True" />
107 </test>
108 <test>
109 <param ftype="fasta.gz" name="input" value="yac.fasta.gz" />
110 <param name="min" value="18" />
111 <param name="max" value="29" />
112 <param name="clip_source_list" value="prebuilt" />
113 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
114 <param name="out_format" value="fasta" />
115 <param name="Nmode" value="accept" />
116 <output file="out.fasta" name="output" />
117 </test>
118 <test>
119 <param ftype="fasta.gz" name="input" value="yac.fasta.gz" />
120 <param name="min" value="18" />
121 <param name="max" value="29" />
122 <param name="clip_source_list" value="prebuilt" />
123 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
124 <param name="Nmode" value="accept" />
125 <param name="out_format" value="fastagz" />
126 <output file="out.fasta.gz" name="output" decompress="True" />
69 </test> 127 </test>
70 </tests> 128 </tests>
71 <help> 129 <help>
72 130
73 **What it does** 131 **What it does**
79 137
80 ------- 138 -------
81 139
82 **Inputs** 140 **Inputs**
83 141
84 1. A fastq file of reads to be clipped 142 1. A fastq or fasta file of reads to be clipped
85 2. Select the size of the reads to be kept 143 2. Select the size of the reads to be kept
86 3. Select an output format when input is a fastq file (this may be fastq or fastq) 144 3. Select an output format. When input is a fastq file, this may be fastq or fasta, whereas
145 when input is a fasta file, this only may be a fasta.
87 4. Select whether you wish or do not wish to keep clipped sequences with unknown nucleotides (N) 146 4. Select whether you wish or do not wish to keep clipped sequences with unknown nucleotides (N)
88 5. Select a pre-built adapter sequence or enter your own sequence (at least 7 nucleotides long) 147 5. Select a pre-built adapter sequence or enter your own sequence (at least 7 nucleotides long)
89 148
90 ------- 149 -------
91 150