Mercurial > repos > brenninc > tagdust_2_31
comparison macros.xml @ 0:40c86e14b674 draft
Uploaded first version of tagdust
author | brenninc |
---|---|
date | Mon, 09 May 2016 04:08:01 -0400 |
parents | |
children | da90c37031bb |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:40c86e14b674 |
---|---|
1 <?xml version="1.0"?> | |
2 <macros> | |
3 <xml name="requirements"> | |
4 <requirements> | |
5 <requirement type="package" version="2.31">tagdust</requirement> | |
6 </requirements> | |
7 </xml> | |
8 <xml name="version_command"> | |
9 <version_command>tagdust --version | head -n 1 | awk '{ print $2 }'</version_command> | |
10 </xml> | |
11 <xml name="stdio"> | |
12 <stdio> | |
13 <exit_code range="1:" level="fatal" description="Error" /> | |
14 </stdio> | |
15 </xml> | |
16 <token name="@cat-archiecture@"> | |
17 echo using architecture ; | |
18 cat $architecture.fields.path ; | |
19 echo ; | |
20 </token> | |
21 <token name="@tagdust-call-minus-files@"> | |
22 mkdir output ; | |
23 tagdust -t\${GALAXY_SLOTS:-4} -o output/data | |
24 -arch $architecture.fields.path | |
25 #if $reference_source.reference_source_selector=='history': | |
26 -ref $reference_source.ref_file | |
27 #end if | |
28 #if $reference_source.reference_source_selector=='cached': | |
29 -ref $reference_source.ref_path.fields.path | |
30 #end if | |
31 </token> | |
32 <token name="@ls_and_barcode@"> | |
33 echo files in output folder ; | |
34 ls -al output ; | |
35 #if $include.barcode_files=="yes" | |
36 #if $architecture.fields.barcode=="yes" | |
37 cd output ; | |
38 ls *_BC_* > $barcode_files | |
39 #else | |
40 echo Selected architecture not expected to generate any barcode files > $barcode_files ; | |
41 echo To avoid this output set Choose to find the barcode files to No >> $barcode_files ; | |
42 #end if | |
43 #else | |
44 #if $architecture.fields.barcode=="yes" | |
45 echo ; | |
46 echo Tagdust not included in output at users request! ; | |
47 echo To get then set Choose to find the barcode files to Yes and run the tool again ; | |
48 #end if | |
49 #end if | |
50 </token> | |
51 <xml name="architecture"> | |
52 <param name="architecture" type="select" label="Using architecture"> | |
53 <options from_data_table="tagdust_architecture"/> | |
54 <validator type="no_options" message="No architecture found"/> | |
55 <!--filter name="barcode" value="yes" column="3"/--> | |
56 </param> | |
57 </xml> | |
58 <xml name="reference_source"> | |
59 <conditional name="reference_source"> | |
60 <param name="reference_source_selector" type="select" label="Choose the source for the reference fasta (If any)"> | |
61 <option value="none" selected="true">Do not include a reference fasta</option> | |
62 <option value="cached">Locally cached</option> | |
63 <option value="history">History</option> | |
64 </param> | |
65 <when value="none"/> | |
66 <when value="cached"> | |
67 <param name="ref_path" type="select" label="Using reference fasta"> | |
68 <options from_data_table="all_fasta"/> | |
69 <validator type="no_options" message="A built-in reference fasta is not available for the build associated with the selected input file"/> | |
70 </param> | |
71 </when> | |
72 <when value="history"> | |
73 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
74 </when> | |
75 </conditional> | |
76 </xml> | |
77 <xml name="include_barcode_file"> | |
78 <conditional name="include"> | |
79 <param name="barcode_files" type="select" label="Choose to find the barcode files (If any)"> | |
80 <option value="yes" selected="true">Yes. Look for possible barcode separated files.</option> | |
81 <option value="no" >No. Ignores all barcode files even if these are generated.</option> | |
82 </param> | |
83 <when value="yes"/> | |
84 <when value="no"/> | |
85 </conditional> | |
86 </xml> | |
87 <xml name="output_barcode"> | |
88 <data format="txt" name="barcode_files" label="Tagdust barcoded reads."> | |
89 <discover_datasets pattern="data_BC_(?P<designation>.+)\.fq" ext="fastq" directory="output" visible="true" /> | |
90 <filter>(include['barcode_files']=='yes')</filter> | |
91 </data> | |
92 </xml> | |
93 <token name="@tool-documentation@"> | |
94 <![CDATA[ | |
95 | |
96 Note: Output from Architecture with could have a Barcode HMM building block choose to find the barcode files. | |
97 ....If no barcode files are found this will simply be empty. | |
98 ....You may have refresh the history for all barcode files to show. | |
99 | |
100 Please contact the admin to add an architecture / HMM building blocks. | |
101 (There is Data Manager that they can use) | |
102 | |
103 ]]> | |
104 </token> | |
105 <token name="@tagdust-documentation@"> | |
106 <![CDATA[ | |
107 ==== | |
108 | |
109 Taken from The TagDust2 Manual http://tagdust.sourceforge.net (part of Version 2_31 download) | |
110 | |
111 Raw sequences produced by next generation sequencing (NGS) machines can contain adapter, linker, | |
112 barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the sequences | |
113 to be mapped in downstream pipelines. | |
114 TagDust allows users to specify the expected architecture of a read and converts it into a hidden | |
115 Markov model. The latter can assign sequences to a particular barcode (or index) even in the presence | |
116 of sequencing errors. Sequences not matching the architecture (primer dimers, contaminants etc.) are | |
117 automatically discarded | |
118 | |
119 TagDust requires an input file containing sequences and a user defined HMM architecture used to ex- | |
120 tract the reads. The architecture is composed of a selection of pre-defined building blocks representing | |
121 indices, barcodes, spacers and other sequences one might encounter in the raw output of a sequenced | |
122 sample. | |
123 | |
124 HMM Building Blocks | |
125 | |
126 TagDust comes with a set of pre-defined HMM building blocks. Each includes a silent state at the | |
127 beginning and end used to link blocks together. Each block is specified by a unique letter following | |
128 by a colon and some information about the sequence. | |
129 | |
130 Read | |
131 Segment modeling the read. | |
132 Code: R:N | |
133 | |
134 Optional | |
135 Segment modeling an optional single or short stretch of nucleotides. | |
136 Code: O:N | |
137 | |
138 G addition | |
139 Segment modeling the occasional addition of guanines to the reads. | |
140 (89.3% chance of a single G , 19.5% chance of 2 Gs..). | |
141 Code: G:G | |
142 | |
143 Barcode or Index | |
144 Segment modeling a set of barcode sequences. For each sequence a separate HMM is created. The | |
145 barcode sequences must be given as a comma separated list. A null model of the same length as the | |
146 barcode is automatically added and initialized to the background nucleotide frequencies. | |
147 Code: B:GTA,AAC | |
148 | |
149 Fingerprint or Unique Molecular Identifier - UMI | |
150 Segment modeling a fingerprint (or unique molecular identifiers). Insertions and deletions are by | |
151 default not allowed within a fingerprint segment. | |
152 Code: F:NNN | |
153 | |
154 Spacer | |
155 Segment modeling a pre-defined sequence. | |
156 Code: S:GTA | |
157 | |
158 Partial | |
159 This segment is used to model sequences that may only be partially present at the 5‘ or 3‘ end of | |
160 the read. The transition probabilities (orange and blue) are set automatically based on the length | |
161 distribution of exactly matching adapters. | |
162 Code: P:CCTTAA | |
163 ]]> | |
164 </token> | |
165 <xml name="citations"> | |
166 <citations> | |
167 <citation type="bibtex"> | |
168 @misc{ | |
169 TagDust, | |
170 author = {Timo Lassmann}, | |
171 title = {TagDust on sourceforge}, | |
172 url = {http://tagdust.sourceforge.net/} | |
173 } | |
174 </citation> | |
175 <citation type="doi">10.1093/bioinformatics/btp527</citation> | |
176 <citation type="doi">10.1186/s12859-015-0454-y</citation> | |
177 </citations> | |
178 </xml> | |
179 </macros> |