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comparison demultiplex.xml @ 0:cb08a27e5fc2 draft

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author davidvanzessen
date Mon, 29 Aug 2016 05:44:57 -0400
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1 <tool id="demultiplex" name="Demultiplex" version="1.0">
2 <description> </description>
3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements>
6 <command interpreter="bash">
7 wrapper.sh "$input" "$out_file" "$out_file.files_path" "$where" "$mismatches" "$partial" "$input.name"
8 #for $i, $b in enumerate($barcodes)
9 "$b.id"
10 "$b.mid"
11 "$b.trim_start"
12 "$b.trim_end"
13 #end for
14 </command>
15 <inputs>
16 <param name="input" type="data" label="File to split" />
17 <repeat name="barcodes" title="Barcodes" min="1" default="1">
18 <param name="id" type="text" size="50" label="ID" />
19 <param name="mid" type="select" label="Mid">
20 <option value="ACGAGTGCGT">MID-1</option>
21 <option value="ACGCACTCGT">MID-1 reverse complement</option>
22 <option value="ACGCTCGACA">MID-2</option>
23 <option value="TGTCGAGCGT">MID-2 reverse complement</option>
24 <option value="AGACGCACTC">MID-3</option>
25 <option value="GAGTGCGTCT">MID-3 reverse complement</option>
26 <option value="AGCACTGTAG">MID-4</option>
27 <option value="CTACAGTGCT">MID-4 reverse complement</option>
28 <option value="ATCAGACACG">MID-5</option>
29 <option value="CGTGTCTGAT">MID-5 reverse complement</option>
30 <option value="ATATCGCGAG">MID-6</option>
31 <option value="CTCGCGATAT">MID-6 reverse complement</option>
32 <option value="CGTGTCTCTA">MID-7</option>
33 <option value="TAGAGACACG">MID-7 reverse complement</option>
34 <option value="CTCGCGTGTC">MID-8</option>
35 <option value="GACACGCGAG">MID-8 reverse complement</option>
36 <option value="TCTCTATGCG">MID-10</option>
37 <option value="CGCATAGAGA">MID-10 reverse complement</option>
38 <option value="TGATACGTCT">MID-11</option>
39 <option value="AGACGTATCA">MID-11 reverse complement</option>
40 <option value="CATAGTAGTG">MID-13</option>
41 <option value="CACTACTATG">MID-13 reverse complement</option>
42 <option value="CGAGAGATAC">MID-14</option>
43 <option value="GTATCTCTCG">MID-14 reverse complement</option>
44 <option value="ATACGACGTA">MID-15</option>
45 <option value="TACGTCGTAT">MID-15 reverse complement</option>
46 <option value="TCACGTACTA">MID-16</option>
47 <option value="TAGTACGTGA">MID-16 reverse complement</option>
48 <option value="CGTCTAGTAC">MID-17</option>
49 <option value="GTACTAGACG">MID-17 reverse complement</option>
50 <option value="TCTACGTAGC">MID-18</option>
51 <option value="GCTACGTAGA">MID-18 reverse complement</option>
52 <option value="TGTACTACTC">MID-19</option>
53 <option value="GAGTAGTACA">MID-19 reverse complement</option>
54 <option value="ACGACTACAG">MID-20</option>
55 <option value="CTGTAGTCGT">MID-20 reverse complement</option>
56 <option value="CGTAGACTAG">MID-21</option>
57 <option value="CTAGTCTACG">MID-21 reverse complement</option>
58 <option value="TACGAGTATG">MID-22</option>
59 <option value="CATACTCGTA">MID-22 reverse complement</option>
60 <option value="TACTCTCGTG">MID-23</option>
61 <option value="CACGAGAGTA">MID-23 reverse complement</option>
62 <option value="TAGAGACGAG">MID-24</option>
63 <option value="CTCGTCTCTA">MID-24 reverse complement</option>
64 <option value="TCGTCGCTCG">MID-25</option>
65 <option value="CGAGCGACGA">MID-25 reverse complement</option>
66 <option value="ACATACGCGT">MID-26</option>
67 <option value="ACGCGTATGT">MID-26 reverse complement</option>
68 <option value="ACGCGAGTAT">MID-27</option>
69 <option value="ATACTCGCGT">MID-27 reverse complement</option>
70 <option value="ACTACTATGT">MID-28</option>
71 <option value="ACATAGTAGT">MID-28 reverse complement</option>
72 <option value="ACTGTACAGT">MID-29</option>
73 <option value="ACTGTACAGT">MID-29 reverse complement</option>
74 <option value="AGACTATACT">MID-30</option>
75 <option value="AGTATAGTCT">MID-30 reverse complement</option>
76 <option value="AGCGTCGTCT">MID-31</option>
77 <option value="AGACGACGCT">MID-31 reverse complement</option>
78 <option value="AGTACGCTAT">MID-32</option>
79 <option value="ATAGCGTACT">MID-32 reverse complement</option>
80 <option value="ATAGAGTACT">MID-33</option>
81 <option value="AGTACTCTAT">MID-33 reverse complement</option>
82 <option value="CACGCTACGT">MID-34</option>
83 <option value="ACGTAGCGTG">MID-34 reverse complement</option>
84 <option value="CAGTAGACGT">MID-35</option>
85 <option value="ACGTCTACTG">MID-35 reverse complement</option>
86 <option value="CGACGTGACT">MID-36</option>
87 <option value="AGTCACGTCG">MID-36 reverse complement</option>
88 <option value="TACACACACT">MID-37</option>
89 <option value="AGTGTGTGTA">MID-37 reverse complement</option>
90 <option value="TACACGTGAT">MID-38</option>
91 <option value="ATCACGTGTA">MID-38 reverse complement</option>
92 <option value="TACAGATCGT">MID-39</option>
93 <option value="ACGATCTGTA">MID-39 reverse complement</option>
94 <option value="TACGCTGTCT">MID-40</option>
95 <option value="AGACAGCGTA">MID-40 reverse complement</option>
96 <option value="TAGTGTAGAT">MID-41</option>
97 <option value="ATCTACACTA">MID-41 reverse complement</option>
98 <option value="TCGATCACGT">MID-42</option>
99 <option value="ACGTGATCGA">MID-42 reverse complement</option>
100 <option value="TCGCACTAGT">MID-43</option>
101 <option value="ACTAGTGCGA">MID-43 reverse complement</option>
102 <option value="TCTAGCGACT">MID-44</option>
103 <option value="AGTCGCTAGA">MID-44 reverse complement</option>
104 <option value="TCTATACTAT">MID-45</option>
105 <option value="ATAGTATAGA">MID-45 reverse complement</option>
106 <option value="TGACGTATGT">MID-46</option>
107 <option value="ACATACGTCA">MID-46 reverse complement</option>
108 <option value="TGTGAGTAGT">MID-47</option>
109 <option value="ACTACTCACA">MID-47 reverse complement</option>
110 <option value="ACAGTATATA">MID-48</option>
111 <option value="TATATACTGT">MID-48 reverse complement</option>
112 <option value="ACGCGATCGA">MID-49</option>
113 <option value="TCGATCGCGT">MID-49 reverse complement</option>
114 <option value="ACTAGCAGTA">MID-50</option>
115 <option value="TACTGCTAGT">MID-50 reverse complement</option>
116 <option value="AGCTCACGTA">MID-51</option>
117 <option value="TACGTGAGCT">MID-51 reverse complement</option>
118 <option value="AGTATACATA">MID-52</option>
119 <option value="TATGTATACT">MID-52 reverse complement</option>
120 <option value="AGTCGAGAGA">MID-53</option>
121 <option value="TCTCTCGACT">MID-53 reverse complement</option>
122 <option value="AGTGCTACGA">MID-54</option>
123 <option value="TCGTAGCACT">MID-54 reverse complement</option>
124 <option value="CGATCGTATA">MID-55</option>
125 <option value="TATACGATCG">MID-55 reverse complement</option>
126 <option value="CGCAGTACGA">MID-56</option>
127 <option value="TCGTACTGCG">MID-56 reverse complement</option>
128 <option value="CGCGTATACA">MID-57</option>
129 <option value="TGTATACGCG">MID-57 reverse complement</option>
130 <option value="CGTACAGTCA">MID-58</option>
131 <option value="TGACTGTACG">MID-58 reverse complement</option>
132 <option value="CGTACTCAGA">MID-59</option>
133 <option value="TCTGAGTACG">MID-59 reverse complement</option>
134 <option value="CTACGCTCTA">MID-60</option>
135 <option value="TAGAGCGTAG">MID-60 reverse complement</option>
136 <option value="CTATAGCGTA">MID-61</option>
137 <option value="TACGCTATAG">MID-61 reverse complement</option>
138 <option value="TACGTCATCA">MID-62</option>
139 <option value="TGATGACGTA">MID-62 reverse complement</option>
140 <option value="TAGTCGCATA">MID-63</option>
141 <option value="TATGCGACTA">MID-63 reverse complement</option>
142 <option value="TATATATACA">MID-64</option>
143 <option value="TGTATATATA">MID-64 reverse complement</option>
144 <option value="TATGCTAGTA">MID-65</option>
145 <option value="TACTAGCATA">MID-65 reverse complement</option>
146 <option value="TCACGCGAGA">MID-66</option>
147 <option value="TCTCGCGTGA">MID-66 reverse complement</option>
148 <option value="TCGATAGTGA">MID-67</option>
149 <option value="TCACTATCGA">MID-67 reverse complement</option>
150 <option value="TCGCTGCGTA">MID-68</option>
151 <option value="TACGCAGCGA">MID-68 reverse complement</option>
152 <option value="TCTGACGTCA">MID-69</option>
153 <option value="TGACGTCAGA">MID-69 reverse complement</option>
154 <option value="TGAGTCAGTA">MID-70</option>
155 <option value="TACTGACTCA">MID-70 reverse complement</option>
156 <option value="TGTAGTGTGA">MID-71</option>
157 <option value="TCACACTACA">MID-71 reverse complement</option>
158 <option value="TGTCACACGA">MID-72</option>
159 <option value="TCGTGTGACA">MID-72 reverse complement</option>
160 <option value="TGTCGTCGCA">MID-73</option>
161 <option value="TGCGACGACA">MID-73 reverse complement</option>
162 <option value="ACACATACGC">MID-74</option>
163 <option value="GCGTATGTGT">MID-74 reverse complement</option>
164 <option value="ACAGTCGTGC">MID-75</option>
165 <option value="GCACGACTGT">MID-75 reverse complement</option>
166 <option value="ACATGACGAC">MID-76</option>
167 <option value="GTCGTCATGT">MID-76 reverse complement</option>
168 <option value="ACGACAGCTC">MID-77</option>
169 <option value="GAGCTGTCGT">MID-77 reverse complement</option>
170 <option value="ACGTCTCATC">MID-78</option>
171 <option value="GATGAGACGT">MID-78 reverse complement</option>
172 <option value="ACTCATCTAC">MID-79</option>
173 <option value="GTAGATGAGT">MID-79 reverse complement</option>
174 <option value="ACTCGCGCAC">MID-80</option>
175 <option value="GTGCGCGAGT">MID-80 reverse complement</option>
176 <option value="AGAGCGTCAC">MID-81</option>
177 <option value="GTGACGCTCT">MID-81 reverse complement</option>
178 <option value="AGCGACTAGC">MID-82</option>
179 <option value="GCTAGTCGCT">MID-82 reverse complement</option>
180 <option value="AGTAGTGATC">MID-83</option>
181 <option value="GATCACTACT">MID-83 reverse complement</option>
182 <option value="AGTGACACAC">MID-84</option>
183 <option value="GTGTGTCACT">MID-84 reverse complement</option>
184 <option value="AGTGTATGTC">MID-85</option>
185 <option value="GACATACACT">MID-85 reverse complement</option>
186 <option value="ATAGATAGAC">MID-86</option>
187 <option value="GTCTATCTAT">MID-86 reverse complement</option>
188 <option value="ATATAGTCGC">MID-87</option>
189 <option value="GCGACTATAT">MID-87 reverse complement</option>
190 <option value="ATCTACTGAC">MID-88</option>
191 <option value="GTCAGTAGAT">MID-88 reverse complement</option>
192 <option value="CACGTAGATC">MID-89</option>
193 <option value="GATCTACGTG">MID-89 reverse complement</option>
194 <option value="CACGTGTCGC">MID-90</option>
195 <option value="GCGACACGTG">MID-90 reverse complement</option>
196 <option value="CATACTCTAC">MID-91</option>
197 <option value="GTAGAGTATG">MID-91 reverse complement</option>
198 <option value="CGACACTATC">MID-92</option>
199 <option value="GATAGTGTCG">MID-92 reverse complement</option>
200 <option value="CGAGACGCGC">MID-93</option>
201 <option value="GCGCGTCTCG">MID-93 reverse complement</option>
202 <option value="CGTATGCGAC">MID-94</option>
203 <option value="GTCGCATACG">MID-94 reverse complement</option>
204 <option value="CGTCGATCTC">MID-95</option>
205 <option value="GAGATCGACG">MID-95 reverse complement</option>
206 <option value="CTACGACTGC">MID-96</option>
207 <option value="GCAGTCGTAG">MID-96 reverse complement</option>
208 <option value="CTAGTCACTC">MID-97</option>
209 <option value="GAGTGACTAG">MID-97 reverse complement</option>
210 <option value="CTCTACGCTC">MID-98</option>
211 <option value="GAGCGTAGAG">MID-98 reverse complement</option>
212 <option value="CTGTACATAC">MID-99</option>
213 <option value="GTATGTACAG">MID-99 reverse complement</option>
214 <option value="TAGACTGCAC">MID-100</option>
215 <option value="GTGCAGTCTA">MID-100 reverse complement</option>
216 <option value="TAGCGCGCGC">MID-101</option>
217 <option value="GCGCGCGCTA">MID-101 reverse complement</option>
218 <option value="TAGCTCTATC">MID-102</option>
219 <option value="GATAGAGCTA">MID-102 reverse complement</option>
220 <option value="TATAGACATC">MID-103</option>
221 <option value="GATGTCTATA">MID-103 reverse complement</option>
222 <option value="TATGATACGC">MID-104</option>
223 <option value="GCGTATCATA">MID-104 reverse complement</option>
224 <option value="TCACTCATAC">MID-105</option>
225 <option value="GTATGAGTGA">MID-105 reverse complement</option>
226 <option value="TCATCGAGTC">MID-106</option>
227 <option value="GACTCGATGA">MID-106 reverse complement</option>
228 <option value="TCGAGCTCTC">MID-107</option>
229 <option value="GAGAGCTCGA">MID-107 reverse complement</option>
230 <option value="TCGCAGACAC">MID-108</option>
231 <option value="GTGTCTGCGA">MID-108 reverse complement</option>
232 <option value="TCTGTCTCGC">MID-109</option>
233 <option value="GCGAGACAGA">MID-109 reverse complement</option>
234 <option value="TGAGTGACGC">MID-110</option>
235 <option value="GCGTCACTCA">MID-110 reverse complement</option>
236 <option value="TGATGTGTAC">MID-111</option>
237 <option value="GTACACATCA">MID-111 reverse complement</option>
238 <option value="TGCTATAGAC">MID-112</option>
239 <option value="GTCTATAGCA">MID-112 reverse complement</option>
240 <option value="TGCTCGCTAC">MID-113</option>
241 <option value="GTAGCGAGCA">MID-113 reverse complement</option>
242 <option value="ACGTGCAGCG">MID-114</option>
243 <option value="CGCTGCACGT">MID-114 reverse complement</option>
244 <option value="ACTCACAGAG">MID-115</option>
245 <option value="CTCTGTGAGT">MID-115 reverse complement</option>
246 <option value="AGACTCAGCG">MID-116</option>
247 <option value="CGCTGAGTCT">MID-116 reverse complement</option>
248 <option value="AGAGAGTGTG">MID-117</option>
249 <option value="CACACTCTCT">MID-117 reverse complement</option>
250 <option value="AGCTATCGCG">MID-118</option>
251 <option value="CGCGATAGCT">MID-118 reverse complement</option>
252 <option value="AGTCTGACTG">MID-119</option>
253 <option value="CAGTCAGACT">MID-119 reverse complement</option>
254 <option value="AGTGAGCTCG">MID-120</option>
255 <option value="CGAGCTCACT">MID-120 reverse complement</option>
256 <option value="ATAGCTCTCG">MID-121</option>
257 <option value="CGAGAGCTAT">MID-121 reverse complement</option>
258 <option value="ATCACGTGCG">MID-122</option>
259 <option value="CGCACGTGAT">MID-122 reverse complement</option>
260 <option value="ATCGTAGCAG">MID-123</option>
261 <option value="CTGCTACGAT">MID-123 reverse complement</option>
262 <option value="ATCGTCTGTG">MID-124</option>
263 <option value="CACAGACGAT">MID-124 reverse complement</option>
264 <option value="ATGTACGATG">MID-125</option>
265 <option value="CATCGTACAT">MID-125 reverse complement</option>
266 <option value="ATGTGTCTAG">MID-126</option>
267 <option value="CTAGACACAT">MID-126 reverse complement</option>
268 <option value="CACACGATAG">MID-127</option>
269 <option value="CTATCGTGTG">MID-127 reverse complement</option>
270 <option value="CACTCGCACG">MID-128</option>
271 <option value="CGTGCGAGTG">MID-128 reverse complement</option>
272 <option value="CAGACGTCTG">MID-129</option>
273 <option value="CAGACGTCTG">MID-129 reverse complement</option>
274 <option value="CAGTACTGCG">MID-130</option>
275 <option value="CGCAGTACTG">MID-130 reverse complement</option>
276 <option value="CGACAGCGAG">MID-131</option>
277 <option value="CTCGCTGTCG">MID-131 reverse complement</option>
278 <option value="CGATCTGTCG">MID-132</option>
279 <option value="CGACAGATCG">MID-132 reverse complement</option>
280 <option value="CGCGTGCTAG">MID-133</option>
281 <option value="CTAGCACGCG">MID-133 reverse complement</option>
282 <option value="CGCTCGAGTG">MID-134</option>
283 <option value="CACTCGAGCG">MID-134 reverse complement</option>
284 <option value="CGTGATGACG">MID-135</option>
285 <option value="CGTCATCACG">MID-135 reverse complement</option>
286 <option value="CTATGTACAG">MID-136</option>
287 <option value="CTGTACATAG">MID-136 reverse complement</option>
288 <option value="CTCGATATAG">MID-137</option>
289 <option value="CTATATCGAG">MID-137 reverse complement</option>
290 <option value="CTCGCACGCG">MID-138</option>
291 <option value="CGCGTGCGAG">MID-138 reverse complement</option>
292 <option value="CTGCGTCACG">MID-139</option>
293 <option value="CGTGACGCAG">MID-139 reverse complement</option>
294 <option value="CTGTGCGTCG">MID-140</option>
295 <option value="CGACGCACAG">MID-140 reverse complement</option>
296 <option value="TAGCATACTG">MID-141</option>
297 <option value="CAGTATGCTA">MID-141 reverse complement</option>
298 <option value="TATACATGTG">MID-142</option>
299 <option value="CACATGTATA">MID-142 reverse complement</option>
300 <option value="TATCACTCAG">MID-143</option>
301 <option value="CTGAGTGATA">MID-143 reverse complement</option>
302 <option value="TATCTGATAG">MID-144</option>
303 <option value="CTATCAGATA">MID-144 reverse complement</option>
304 <option value="TCGTGACATG">MID-145</option>
305 <option value="CATGTCACGA">MID-145 reverse complement</option>
306 <option value="TCTGATCGAG">MID-146</option>
307 <option value="CTCGATCAGA">MID-146 reverse complement</option>
308 <option value="TGACATCTCG">MID-147</option>
309 <option value="CGAGATGTCA">MID-147 reverse complement</option>
310 <option value="TGAGCTAGAG">MID-148</option>
311 <option value="CTCTAGCTCA">MID-148 reverse complement</option>
312 <option value="TGATAGAGCG">MID-149</option>
313 <option value="CGCTCTATCA">MID-149 reverse complement</option>
314 <option value="TGCGTGTGCG">MID-150</option>
315 <option value="CGCACACGCA">MID-150 reverse complement</option>
316 <option value="TGCTAGTCAG">MID-151</option>
317 <option value="CTGACTAGCA">MID-151 reverse complement</option>
318 <option value="TGTATCACAG">MID-152</option>
319 <option value="CTGTGATACA">MID-152 reverse complement</option>
320 <option value="TGTGCGCGTG">MID-153</option>
321 <option value="CACGCGCACA">MID-153 reverse complement</option>
322 </param>
323
324 <param name="trim_start" type="integer" size="3" value="0" label="How many nucleotides to trim from the start" />
325
326 <param name="trim_end" type="integer" size="3" value="0" label="How many nucleotides to trim from the end" />
327 </repeat>
328
329 <param name="where" type="select" label="Barcodes found at">
330 <option value="bol">Start: 5' end</option>
331 <option value="eol">End: 3' end</option>
332 </param>
333
334 <param name="mismatches" type="integer" size="3" value="2" label="Max. number of mismatches allowed." />
335
336 <param name="partial" type="integer" size="3" value="0" label="Allow partial overlap of barcodes." />
337
338 </inputs>
339 <outputs>
340 <data format="html" name="out_file" />
341 </outputs>
342 <help>
343 - Splitting sff or fastq files into FASTQ, FASTA and (optional) trimmed FASTA files with a FASTQC report on the FASTQ file, this tool uses:
344 - sff2fastq (https://github.com/indraniel/sff2fastq) to extract a fastq file.
345 - fastx_barcode_splitter.pl (http://hannonlab.cshl.edu/fastx_toolkit/commandline.html) to demultiplex.
346 - fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to provide analysis of the fastq files.
347
348 </help>
349 </tool>