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comparison sickle.xml @ 5:3905ccd5c631 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
author iuc
date Thu, 13 Apr 2017 16:06:10 -0400
parents edaa8572219d
children 6756c87dc2d4
comparison
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4:edaa8572219d 5:3905ccd5c631
1 <tool id="sickle" name="Sickle" version="1.33"> 1 <tool id="sickle" name="Sickle" version="1.33.1" profile="17.01">
2 <description>windowed adaptive trimming of FASTQ data</description> 2 <description>windowed adaptive trimming of FASTQ data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.33">sickle</requirement> 4 <requirement type="package" version="1.33">sickle</requirement>
5 <!-- conda dependency --> 5 <!-- conda dependency -->
6 <requirement type="package" version="1.33">sickle-trim</requirement> 6 <requirement type="package" version="1.33">sickle-trim</requirement>
7 </requirements> 7 </requirements>
8 <version_command>sickle --version | head -n 1</version_command> 8 <version_command>sickle --version | head -n 1</version_command>
9 <command> 9 <command><![CDATA[
10 ## Link in the input files, which also determines the type of the output
11 #set compressed = ""
12 #if str($readtype.single_or_paired) == "se":
13 #if $readtype.input_single.is_of_type('fastq.gz'):
14 #set read1 = "input_1.fastq.gz"
15 #set compressed = "-g"
16 #else
17 #set read1 = "input_1.fastq"
18 #end if
19 ln -f -s '${readtype.input_single}' ${read1} &&
20 #else if str($readtype.single_or_paired) == "pe_combo":
21 #if $readtype.input_combo.is_of_type('fastq.gz'):
22 #set read1 = "input_1.fastq.gz"
23 #set compressed = "-g"
24 #else
25 #set read1 = "input_1.fastq"
26 #end if
27 ln -f -s '${readtype.input_combo}' ${read1} &&
28 #else if str($readtype.single_or_paired) == "pe_sep":
29 #if $readtype.input_paired1.is_of_type('fastq.gz'):
30 #set read1 = "input_1.fastq.gz"
31 #set compressed = "-g"
32 #else
33 #set read1 = "input_1.fastq"
34 #end if
35 ln -f -s '${readtype.input_paired1}' ${read1} &&
36
37 #if $readtype.input_paired2.is_of_type('fastq.gz'):
38 #set read2 = "input_2.fastq.gz"
39 #else
40 #set read2 = "input_2.fastq"
41 #end if
42 ln -f -s '${readtype.input_paired2}' ${read2} &&
43 #else
44 #if $readtype.input_paired.forward.is_of_type('fastq.gz'):
45 #set read1 = "input_1.fastq.gz"
46 #set compressed = "-g"
47 #else
48 #set read1 = "input_1.fastq"
49 #end if
50 ln -f -s '${readtype.input_paired.forward}' ${read1} &&
51
52 #if $readtype.input_paired.reverse.is_of_type('fastq.gz'):
53 #set read2 = "input_2.fastq.gz"
54 #else
55 #set read2 = "input_2.fastq"
56 #end if
57 ln -f -s '${readtype.input_paired.reverse}' ${read2} &&
58 #end if
59
10 sickle 60 sickle
11 61
12 #if str($readtype.single_or_paired) == "se": 62 #if str($readtype.single_or_paired) == "se":
13 se -f "${readtype.input_single}" -o "$output_single" 63 se -f ${read1} -o '${output_single}'
14 64
15 #if $readtype.input_single.is_of_type('fastqillumina'): 65 #if $readtype.input_single.is_of_type('fastqillumina', 'fastqillumina.gz'):
16 -t illumina 66 -t illumina
17 #else if $readtype.input_single.is_of_type('fastqsolexa'): 67 #else if $readtype.input_single.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
18 -t solexa 68 -t solexa
19 #else: 69 #else:
20 -t sanger 70 -t sanger
21 #end if 71 #end if
22 #end if 72 #else if str($readtype.single_or_paired) == "pe_combo":
23
24 #if str($readtype.single_or_paired) == "pe_combo":
25 #if $readtype.output_n: 73 #if $readtype.output_n:
26 pe -c "${readtype.input_combo}" -M "$output_combo" 74 pe -c ${read1} -M '${output_combo}'
27 #else 75 #else
28 pe -c "${readtype.input_combo}" -m "$output_combo" -s "$output_combo_single" 76 pe -c ${read1} -m '${output_combo}' -s '${output_combo_single}'
29 #end if 77 #end if
30 78
31 #if $readtype.input_combo.is_of_type('fastqillumina'): 79 #if $readtype.input_combo.is_of_type('fastqillumina', 'fastqillumina.gz'):
32 -t illumina 80 -t illumina
33 #else if $readtype.input_combo.is_of_type('fastqsolexa'): 81 #else if $readtype.input_combo.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
34 -t solexa 82 -t solexa
35 #else: 83 #else:
36 -t sanger 84 -t sanger
37 #end if 85 #end if
38 #end if 86 #else if str($readtype.single_or_paired) == "pe_sep":
39 87 pe -f ${read1} -r ${read2} -o '${output_paired1}' -p '${output_paired2}' -s '${output_paired_single}'
40 #if str($readtype.single_or_paired) == "pe_sep": 88
41 pe -f "${readtype.input_paired1}" -r "${readtype.input_paired2}" -o "$output_paired1" -p "$output_paired2" -s "$output_paired_single" 89 #if $readtype.input_paired1.is_of_type('fastqillumina', 'fastqillumina.gz'):
42
43 #if $readtype.input_paired1.is_of_type('fastqillumina'):
44 -t illumina 90 -t illumina
45 #else if $readtype.input_paired1.is_of_type('fastqsolexa'): 91 #else if $readtype.input_paired1.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
46 -t solexa 92 -t solexa
47 #else: 93 #else:
48 -t sanger 94 -t sanger
49 #end if 95 #end if
50 #end if 96 #else if str($readtype.single_or_paired) == "pe_collection":
51 97 pe -f ${read1} -r ${read2} -o '${output_paired_coll.forward}' -p '${output_paired_coll.reverse}' -s '${output_paired_coll_single}'
52 #if str($readtype.single_or_paired) == "pe_collection": 98
53 pe -f "${readtype.input_paired.forward}" -r "${readtype.input_paired.reverse}" -o "${output_paired_coll.forward}" -p "${output_paired_coll.reverse}" -s "$output_paired_coll_single" 99 #if $readtype.input_paired.forward.is_of_type('fastqillumina', 'fastqillumina.gz'):
54
55 #if $readtype.input_paired.forward.is_of_type('fastqillumina'):
56 -t illumina 100 -t illumina
57 #else if $readtype.input_paired.forward.is_of_type('fastqsolexa'): 101 #else if $readtype.input_paired.forward.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
58 -t solexa 102 -t solexa
59 #else: 103 #else:
60 -t sanger 104 -t sanger
61 #end if 105 #end if
62 #end if 106 #end if
63 107
108 $compressed
109
64 #if str($qual_threshold) != "": 110 #if str($qual_threshold) != "":
65 -q $qual_threshold 111 -q $qual_threshold
66 #end if 112 #end if
67 113
68 #if str($length_threshold) != "": 114 #if str($length_threshold) != "":
74 #end if 120 #end if
75 121
76 #if $trunc_n: 122 #if $trunc_n:
77 -n 123 -n
78 #end if 124 #end if
125 ]]>
79 </command> 126 </command>
80 127
81 <inputs> 128 <inputs>
82 <conditional name="readtype"> 129 <conditional name="readtype">
83 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?" help="Note: Sickle will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger."> 130 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?" help="Note: Sickle will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger.">
86 <option value="pe_sep">Paired-end (two separate input files)</option> 133 <option value="pe_sep">Paired-end (two separate input files)</option>
87 <option value="pe_collection">Paired-end (as collection)</option> 134 <option value="pe_collection">Paired-end (as collection)</option>
88 </param> 135 </param>
89 136
90 <when value="se"> 137 <when value="se">
91 <param format="fastq" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)" /> 138 <param format="fastq,fastq.gz" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)" />
92 </when> 139 </when>
93 140
94 <when value="pe_combo"> 141 <when value="pe_combo">
95 <param format="fastq" name="input_combo" type="data" label="Paired-end interleaved FASTQ reads" help="(-c)" /> 142 <param format="fastq,fastq.gz" name="input_combo" type="data" label="Paired-end interleaved FASTQ reads" help="(-c)" />
96 <param name="output_n" type="boolean" label="Output only one file with all reads" help="This will output only one file with all the reads, where the reads that did not pass filter will be replaced with a single 'N', rather than discarded."/> 143 <param name="output_n" type="boolean" label="Output only one file with all reads" help="This will output only one file with all the reads, where the reads that did not pass filter will be replaced with a single 'N', rather than discarded."/>
97 </when> 144 </when>
98 145
99 <when value="pe_sep"> 146 <when value="pe_sep">
100 <param format="fastq" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" /> 147 <param format="fastq,fastq.gz" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" />
101 <param format="fastq" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" /> 148 <param format="fastq,fastq.gz" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" />
102 </when> 149 </when>
103 150
104 <when value="pe_collection"> 151 <when value="pe_collection">
105 <param format="fastq" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection" /> 152 <param format="fastq,fastq.gz" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection" />
106 </when> 153 </when>
107 </conditional> 154 </conditional>
108 155
109 <param name="qual_threshold" value="20" min="0" type="integer" optional="true" label="Quality threshold" help="Threshold for trimming based on average quality in a window (-q)" /> 156 <param name="qual_threshold" value="20" min="0" type="integer" optional="true" label="Quality threshold" help="Threshold for trimming based on average quality in a window (-q)" />
110 157
148 </data> 195 </data>
149 </outputs> 196 </outputs>
150 <tests> 197 <tests>
151 <test> 198 <test>
152 <param name="single_or_paired" value="pe_combo" /> 199 <param name="single_or_paired" value="pe_combo" />
153 <param name="input_combo" ftype="fastqsanger" value="test.fastq" /> 200 <param name="input_combo" ftype="fastqillumina" value="test.fastq" />
154 <param name="qual_threshold" value="34" /> 201 <param name="qual_threshold" value="3" />
155 <output name="output_combo" ftype="fastqsanger" file="output.c1.fastq" /> 202 <output name="output_combo" ftype="fastqillumina" file="output.c1.fastq" />
156 <output name="output_combo_single" ftype="fastqsanger" file="output.s.fastq" /> 203 <output name="output_combo_single" ftype="fastqillumina" file="output.s.fastq" />
157 </test> 204 </test>
158 <test> 205 <test>
159 <param name="single_or_paired" value="pe_combo" /> 206 <param name="single_or_paired" value="pe_combo" />
160 <param name="input_combo" ftype="fastqsanger" value="test.fastq" /> 207 <param name="input_combo" ftype="fastqillumina" value="test.fastq" />
161 <param name="qual_threshold" value="34" /> 208 <param name="qual_threshold" value="3" />
162 <param name="output_n" value="true" /> 209 <param name="output_n" value="true" />
163 <output name="output_combo" ftype="fastqsanger" file="output.c2.fastq" /> 210 <output name="output_combo" ftype="fastqillumina" file="output.c2.fastq" />
164 </test> 211 </test>
165 <test> 212 <test>
166 <param name="single_or_paired" value="pe_sep" /> 213 <param name="single_or_paired" value="pe_sep" />
167 <param name="input_paired1" ftype="fastqsanger" value="test.f.fastq" /> 214 <param name="input_paired1" ftype="fastqillumina" value="test.f.fastq" />
168 <param name="input_paired2" ftype="fastqsanger" value="test.r.fastq" /> 215 <param name="input_paired2" ftype="fastqillumina" value="test.r.fastq" />
169 <param name="qual_threshold" value="34" /> 216 <param name="qual_threshold" value="3" />
170 <output name="output_paired1" ftype="fastqsanger" file="output.f.fastq" /> 217 <output name="output_paired1" ftype="fastqillumina" file="output.f.fastq" />
171 <output name="output_paired2" ftype="fastqsanger" file="output.r.fastq" /> 218 <output name="output_paired2" ftype="fastqillumina" file="output.r.fastq" />
172 <output name="output_paired_single" ftype="fastqsanger" file="output.s.fastq" /> 219 <output name="output_paired_single" ftype="fastqillumina" file="output.s.fastq" />
220 </test>
221 <test> <!-- as above, but gzipped -->
222 <param name="single_or_paired" value="pe_sep" />
223 <param name="input_paired1" ftype="fastqillumina.gz" value="test.f.fastq.gz" />
224 <param name="input_paired2" ftype="fastqillumina.gz" value="test.r.fastq.gz" />
225 <param name="qual_threshold" value="3" />
226 <output name="output_paired1" ftype="fastqillumina.gz" file="output.f.fastq.gz" />
227 <output name="output_paired2" ftype="fastqillumina.gz" file="output.r.fastq.gz" />
228 <output name="output_paired_single" ftype="fastqillumina.gz" file="output.s.fastq.gz" />
173 </test> 229 </test>
174 <test> 230 <test>
175 <param name="single_or_paired" value="pe_collection" /> 231 <param name="single_or_paired" value="pe_collection" />
176 <param name="input_paired"> 232 <param name="input_paired">
177 <collection type="paired"> 233 <collection type="paired">
178 <element name="forward" ftype="fastqsanger" value="test.f.fastq" /> 234 <element name="forward" ftype="fastqillumina" value="test.f.fastq" />
179 <element name="reverse" ftype="fastqsanger" value="test.r.fastq" /> 235 <element name="reverse" ftype="fastqillumina" value="test.r.fastq" />
180 </collection> 236 </collection>
181 </param> 237 </param>
182 <param name="qual_threshold" value="34" /> 238 <param name="qual_threshold" value="3" />
183 <output_collection name="output_paired_coll" type="paired"> 239 <output_collection name="output_paired_coll" type="paired">
184 <element name="forward" ftype="fastqsanger" file="output.f.fastq" /> 240 <element name="forward" ftype="fastqillumina" file="output.f.fastq" />
185 <element name="reverse" ftype="fastqsanger" file="output.r.fastq" /> 241 <element name="reverse" ftype="fastqillumina" file="output.r.fastq" />
186 </output_collection> 242 </output_collection>
187 <output name="output_paired_coll_single" ftype="fastqsanger" file="output.s.fastq" /> 243 <output name="output_paired_coll_single" ftype="fastqillumina" file="output.s.fastq" />
244 </test>
245
246 <test> <!-- as above, but gzipped -->
247 <param name="single_or_paired" value="pe_collection" />
248 <param name="input_paired">
249 <collection type="paired">
250 <element name="forward" ftype="fastqillumina.gz" value="test.f.fastq.gz" />
251 <element name="reverse" ftype="fastqillumina.gz" value="test.r.fastq.gz" />
252 </collection>
253 </param>
254 <param name="qual_threshold" value="3" />
255 <output_collection name="output_paired_coll" type="paired">
256 <element name="forward" ftype="fastqillumina.gz" file="output.f.fastq.gz" />
257 <element name="reverse" ftype="fastqillumina.gz" file="output.r.fastq.gz" />
258 </output_collection>
259 <output name="output_paired_coll_single" ftype="fastqillumina.gz" file="output.s.fastq.gz" />
188 </test> 260 </test>
189 </tests> 261 </tests>
190 <help> 262 <help>
191 **What it does** 263 **What it does**
192 264