Mercurial > repos > devteam > bamtools_filter
comparison bamtools-filter.xml @ 0:db10554eaad9 draft
Uploaded
author | devteam |
---|---|
date | Tue, 09 Dec 2014 15:04:58 -0500 |
parents | |
children | 5e2fe70292a7 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:db10554eaad9 |
---|---|
1 <tool id="bamFilter" name="Filter" version="0.0.1"> | |
2 <description>BAM datasets on a variety of attributes</description> | |
3 <requirements> | |
4 <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement> | |
5 </requirements> | |
6 <command> | |
7 | |
8 cat $script_file > $out_file2; | |
9 | |
10 #for $bam_count, $input_bam in enumerate( $input_bams ): | |
11 ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" && | |
12 ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && | |
13 #end for | |
14 | |
15 bamtools | |
16 filter | |
17 -script $script_file | |
18 | |
19 #for $bam_count, $input_bam in enumerate( $input_bams ): | |
20 -in "localbam_${bam_count}.bam" | |
21 #end for | |
22 -out $out_file1 | |
23 | |
24 </command> | |
25 | |
26 <inputs> | |
27 <repeat name="input_bams" title="BAM dataset(s) to filter" min="1"> | |
28 <param name="input_bam" type="data" format="bam" label="BAM dataset" /> | |
29 </repeat> | |
30 <repeat name="conditions" title="Condition" min="1"> | |
31 <repeat name="filters" title="Filter" min="1"> | |
32 <conditional name="bam_property"> | |
33 <param name="bam_property_selector" type="select" label="Select BAM property to filter on"> | |
34 <option value="alignmentFlag"/> | |
35 <option value="cigar"/> | |
36 <option value="insertSize"/> | |
37 <option value="isDuplicate"/> | |
38 <option value="isFailedQC"/> | |
39 <option value="isFirstMate"/> | |
40 <option value="isMapped"/> | |
41 <option value="isMateMapped"/> | |
42 <option value="isMateReverseStrand"/> | |
43 <option value="isPaired"/> | |
44 <option value="isPrimaryAlignment"/> | |
45 <option value="isProperPair"/> | |
46 <option value="isReverseStrand"/> | |
47 <option value="isSecondMate"/> | |
48 <option selected="True" value="mapQuality"/> | |
49 <option value="matePosition"/> | |
50 <option value="mateReference"/> | |
51 <option value="name"/> | |
52 <option value="position"/> | |
53 <option value="queryBases"/> | |
54 <option value="reference"/> | |
55 <option value="tag"/> | |
56 </param> | |
57 <!-- would be fanstastic to have AND and OR constructs in when statements --> | |
58 <when value="alignmentFlag"> | |
59 <param name="bam_property_value" type="integer" value="3" label="Filter on this alignment flag" help="Default (3) is for a paired read mapped in a proper pair"/> | |
60 </when> | |
61 <when value="cigar"> | |
62 <param name="bam_property_value" type="text" size="10" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/> | |
63 </when> | |
64 <when value="insertSize"> | |
65 <param name="bam_property_value" type="text" size="10" value=">=250" label="Filter on inster size" help="You can use >, <, =, and ! (not) in your expression. E.g., to select pairs with inster size above 250 nt use ">=250""> | |
66 <sanitizer invalid_char=""> | |
67 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> | |
68 </sanitizer> | |
69 </param> | |
70 </when> | |
71 <when value="isDuplicate"> | |
72 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads makwed as duplicates" help="Checked = Read IS Duplicate, Empty = Read is NOT Duplicate" /> | |
73 </when> | |
74 <when value="isFailedQC"> | |
75 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads failing QC" help="Checked = Failed QC, Empty = Passed QC"/> | |
76 </when> | |
77 <when value="isFirstMate"> | |
78 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select first mate in a read pair" help="Checked = is first mate, Empty = is NOT first mate"/> | |
79 </when> | |
80 <when value="isMapped"> | |
81 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Selected mapped reads" help="Checked = Mapped, Empty = NOT mapped"/> | |
82 </when> | |
83 <when value="isMateMapped"> | |
84 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads with mapped mate" help="Checked = Mate IS mapped Empty = Mate is NOT mapped"/> | |
85 </when> | |
86 <when value="isMateReverseStrand"> | |
87 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads with mate on the reverse strand" help="Checked = Mate IS on reverse strand, Empty = Mate is NOT on the reverse strand"/> | |
88 </when> | |
89 <when value="isPaired"> | |
90 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select paired reads" help="Checked = Read IS paired, Empty = Read is NOT paired"/> | |
91 </when> | |
92 <when value="isPrimaryAlignment"> | |
93 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select BAM records for primary alignments" help="Checked = Alignment IS primary, Empty = Alignment is NOT primary"/> | |
94 </when> | |
95 <when value="isProperPair"> | |
96 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select properly paired reads" help="Checked = Read IS in proper pair, Empty = Read is NOT in the proper pair"/> | |
97 </when> | |
98 <when value="isReverseStrand"> | |
99 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads in the reverse strand only" help="Checked = Read IS on the reverse strand, Empty = Read is NOT on the reverse strand"/> | |
100 </when> | |
101 <when value="isSecondMate"> | |
102 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select second mate in a read pair" help="Checked = Read IS second mate, Empty = Read is NOT second mate"/> | |
103 </when> | |
104 <when value="mapQuality"> | |
105 <param name="bam_property_value" type="text" value="20" label="Filter on read mapping quality (phred scale)" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads with mapping quality of at least 30 use ">=30""> | |
106 <sanitizer invalid_char=""> | |
107 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> | |
108 </sanitizer> | |
109 </param> | |
110 </when> | |
111 <when value="matePosition"> | |
112 <param name="bam_property_value" type="text" value="1000000" label="Filter on the position of the mate" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads with mate (second end) mapping after position 1,000,000 use ">1000000""> | |
113 <sanitizer invalid_char=""> | |
114 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> | |
115 </sanitizer> | |
116 </param> | |
117 </when> | |
118 <when value="mateReference"> | |
119 <param name="bam_property_value" type="text" value="chr22" label="Filter on reference name for the mate" help="You can use = and ! (not) in your expression. E.g., to select reads with mates mapping to chrM use "chr22""> | |
120 <sanitizer invalid_char=""> | |
121 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> | |
122 </sanitizer> | |
123 </param> | |
124 </when> | |
125 <when value="name"> | |
126 <param name="bam_property_value" type="text" label="Filter on read name" help="You can use = and ! (not) in your expression."> | |
127 <sanitizer invalid_char=""> | |
128 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> | |
129 </sanitizer> | |
130 </param> | |
131 </when> | |
132 <when value="position"> | |
133 <param name="bam_property_value" type="text" value="500000" label="Filter on the position of the read" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads mapping after position 5,000 use ">5000""> | |
134 <sanitizer invalid_char=""> | |
135 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> | |
136 </sanitizer> | |
137 </param> | |
138 </when> | |
139 <when value="queryBases"> | |
140 <param name="bam_property_value" type="text" value="ttagggttagg" label="Filter on a sequence motif" help="You can use ! (not) in your expression"> | |
141 <sanitizer invalid_char=""> | |
142 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> | |
143 </sanitizer> | |
144 </param> | |
145 </when> | |
146 <when value="reference"> | |
147 <param name="bam_property_value" type="text" value="chr22" label="Filter on the reference name for the read" help="You can use ! (not) in your expression"> | |
148 <sanitizer invalid_char=""> | |
149 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> | |
150 </sanitizer> | |
151 </param> | |
152 </when> | |
153 <when value="tag"> | |
154 <param name="bam_property_value" type="text" value="NM:>1" label="Filter on a particular tag" help="You can use >, <, =, and ! (not). | |
155 Tag name and its value must be separated by ":". E.g., to obtain reads with at least one mismatch use "NM:>1""> | |
156 <sanitizer invalid_char=""> | |
157 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value=":!="/></valid> | |
158 </sanitizer> | |
159 </param> | |
160 </when> | |
161 </conditional> | |
162 </repeat> | |
163 </repeat> | |
164 <conditional name="rule_configuration"> | |
165 <param name="rules_selector" type="boolean" truevalue="true" falsevalue="false" label="Would you like to set rules?" help="Allows complex logical constructs. See Example 4 below." /> | |
166 <when value="true"> | |
167 <param name="rules" type="text" size="20" label="Enter rules here" help="This option can only be used with at least two conditions. Read help below (Example 4) to understand how it works." > | |
168 <sanitizer invalid_char=""> | |
169 <valid initial="string.printable"/> | |
170 </sanitizer> | |
171 </param> | |
172 </when> | |
173 </conditional> | |
174 </inputs> | |
175 | |
176 <configfiles> | |
177 <configfile name="script_file"> | |
178 ##Sets up a json configfile for bamtools filter | |
179 ##If there is more than one condition prints brackets and "filters:" | |
180 #if len( $conditions ) > 1 | |
181 { | |
182 "filters": | |
183 [ | |
184 #end if | |
185 #for $i, $c in enumerate( $conditions, start=1 ) | |
186 { "id": "$i", | |
187 #for $j, $s in enumerate( $c.filters, start=1 ) | |
188 ##The if below takes care of the comma at the end of last condition within group | |
189 #if $j != len( $c.filters) | |
190 "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}", | |
191 #else | |
192 "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}" | |
193 #end if | |
194 #end for | |
195 ##The if below takes care of the comma at the end of last condition within group | |
196 #if $i != len( $conditions ) | |
197 }, | |
198 #else | |
199 } | |
200 #end if | |
201 #end for | |
202 #if len( $conditions ) > 1 | |
203 #if str( $rule_configuration.rules_selector ) == "True": | |
204 ], | |
205 "rule" : "${rule_configuration.rules}" | |
206 #else | |
207 ] | |
208 #end if | |
209 } | |
210 #end if | |
211 </configfile> | |
212 </configfiles> | |
213 | |
214 <outputs> | |
215 <data format="txt" name="out_file2" /> | |
216 <data format="bam" name="out_file1" /> | |
217 </outputs> | |
218 <tests> | |
219 <test> | |
220 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> | |
221 <param name="bam_property_selector" value="mapQuality"/> | |
222 <param name="bam_property_value" value=">20"/> | |
223 <output name="out_file1" file="bamtools-test1.bam" ftype="bam"/> | |
224 </test> | |
225 </tests> | |
226 <help> | |
227 **What is does** | |
228 | |
229 BAMTools filter is a very powerful utility to perform complex filtering of BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). | |
230 | |
231 ----- | |
232 | |
233 **How it works** | |
234 | |
235 The tool use logic relies on the three concepts: (1) input BAM, (2) groups, and (3) filters. | |
236 | |
237 *Input BAM(s)* | |
238 | |
239 The input BAM is self-explanatory. This is the dataset you will be filtering. The tool can accept just one or multiple BAM files. To filter on multiple BAMs just add them by clicking **Add new BAM dataset(s) to filter** | |
240 | |
241 *Conditions and Filters* | |
242 | |
243 Conditions for filtering BAM files can be arranged in **Groups and Filters**. While it can be confusing at first this is what gives ultimate power to this tools. So try to look at the examples we are supplying below. | |
244 | |
245 ----- | |
246 | |
247 **Example 1. Using a single filter** | |
248 | |
249 When filtering on a single condition there is no need to worry about filters and conditions. Just choose a filter from the **Select BAM property to filter on:** dropdown and enter a value (or click a checkbox for binary filters). | |
250 For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below: | |
251 | |
252 .. image:: ${static_path}/images/simple-filter.png | |
253 | |
254 ----- | |
255 | |
256 **Example 2. Using multiple filters** | |
257 | |
258 Now suppose one needs to extract reads that (1) have mapping quality of at least 20, (2) contain at least 1 mismatch, and (3) are mapping onto forward strand only. | |
259 To do so we will use three filters as shown below (multiple filters are added to the interface by clicking on the **Add new Filter** button): | |
260 | |
261 .. image:: ${static_path}/images/multiple-filters.png | |
262 | |
263 In this case (you can see that the three filters are grouped within a single Condition - **Condition 1**) the filter too use logical **AND** to perform filtering. | |
264 In other words only reads that (1) have mapping quality of at least 20 **AND** (2) contain at least 1 mismatch **AND** are mapping onto forward strand will be returned in this example. | |
265 | |
266 ----- | |
267 | |
268 **Example 3. Complex filtering with multiple conditions** | |
269 | |
270 Suppose now you would like to select **either** reads that (**1**) have (*1.1*) no mismatches and (*1.2*) are on the forward strand **OR** (**2**) reads that have (*2.1*) | |
271 at least one mismatch and (*2.2*) are on the reverse strand. In this scenario we have to set up two conditions: (**1**) and (**2**) each with two filters: *1.1* and *1.2* as well as *2.1* and *2.2*. | |
272 The following screenshot expalins how this can be done: | |
273 | |
274 .. image:: ${static_path}/images/complex-filters.png | |
275 | |
276 ----- | |
277 | |
278 **Example 4. Even more complex filtering with Rules** | |
279 | |
280 In the above example we have used two conditions (Condition 1 and Condition 2). Using multiple conditions allows to combine them and a variety of ways to enable even more powerful filtering. | |
281 For example, suppose get all reads that (**1**) do NOT map to mitochondria and either (**2**) have mapping quality over 20, or (**3**) are in properly mapped pairs. The logical rule to enable such | |
282 filtering will look like this:: | |
283 | |
284 !(1) & (2 | 3) | |
285 | |
286 Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy: | |
287 | |
288 .. image:: ${static_path}/images/rule.png | |
289 | |
290 There are three conditions here, each with a single filter. A text entry area that can be opened by clicking on the **Would you like to set rules?** checkbox enables you to enter a rule. | |
291 Here numbers correspond to numbers of conditions as they are shown in the interface. E.g., 1 corresponds to condition 1, 2 to condition 2 and so on... In human language this means:: | |
292 | |
293 NOT condition 1 AND (condition 2 OR condition 3) | |
294 | |
295 ----- | |
296 | |
297 **JSON script file** | |
298 | |
299 This tool produces two outputs. One of the them is a BAM file containing filtered reads. The other is a JSONified script. It can help you to see how your instructions are sent to BAMTools. | |
300 For instance, the example 4 looks like this in the JSON form:: | |
301 | |
302 { | |
303 "filters": | |
304 [ | |
305 { "id": "1", | |
306 "tag":"NM:=0", | |
307 "isReverseStrand":"false" | |
308 }, | |
309 { "id": "2", | |
310 "tag":"NM:>0", | |
311 "isReverseStrand":"true" | |
312 } | |
313 ] | |
314 } | |
315 | |
316 | |
317 | |
318 ----- | |
319 | |
320 **More information** | |
321 | |
322 .. class:: infomark | |
323 | |
324 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki | |
325 | |
326 | |
327 </help> | |
328 <citations> | |
329 <citation type="doi">10.1093/bioinformatics/btr174</citation> | |
330 </citations> | |
331 </tool> |