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comparison bamtools-filter.xml @ 1:5e2fe70292a7 draft

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planemo upload commit 5ad726dc73203a704666033cd3bf70b82575978f-dirty
author devteam
date Wed, 26 Aug 2015 14:58:44 -0400
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2 <description>BAM datasets on a variety of attributes</description> 2 <description>BAM datasets on a variety of attributes</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement> 4 <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7
8 cat $script_file > $out_file2; 7 cat $script_file > $out_file2;
9 8
10 #for $bam_count, $input_bam in enumerate( $input_bams ): 9 #for $bam_count, $input_bam in enumerate( $input_bams ):
11 ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp; 10 ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
12 ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp; 11 ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
13 #end for 12 #end for
14 13
18 17
19 #for $bam_count, $input_bam in enumerate( $input_bams ): 18 #for $bam_count, $input_bam in enumerate( $input_bams ):
20 -in "localbam_${bam_count}.bam" 19 -in "localbam_${bam_count}.bam"
21 #end for 20 #end for
22 -out $out_file1 21 -out $out_file1
23
24 </command> 22 </command>
25
26 <inputs> 23 <inputs>
27 <repeat name="input_bams" title="BAM dataset(s) to filter" min="1"> 24 <repeat name="input_bams" title="BAM dataset(s) to filter" min="1">
28 <param name="input_bam" type="data" format="bam" label="BAM dataset" /> 25 <param name="input_bam" type="data" format="bam" label="BAM dataset" />
29 </repeat> 26 </repeat>
30 <repeat name="conditions" title="Condition" min="1"> 27 <repeat name="conditions" title="Condition" min="1">
195 ##The if below takes care of the comma at the end of last condition within group 192 ##The if below takes care of the comma at the end of last condition within group
196 #if $i != len( $conditions ) 193 #if $i != len( $conditions )
197 }, 194 },
198 #else 195 #else
199 } 196 }
200 #end if 197 #end if
201 #end for 198 #end for
202 #if len( $conditions ) > 1 199 #if len( $conditions ) > 1
203 #if str( $rule_configuration.rules_selector ) == "True": 200 #if str( $rule_configuration.rules_selector ) == "True":
204 ], 201 ],
205 "rule" : "${rule_configuration.rules}" 202 "rule" : "${rule_configuration.rules}"
206 #else 203 #else
247 **Example 1. Using a single filter** 244 **Example 1. Using a single filter**
248 245
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). 246 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: 247 For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below:
251 248
252 .. image:: ${static_path}/images/simple-filter.png 249 .. image:: images/single-filter.png
253 250
254 ----- 251 -----
255 252
256 **Example 2. Using multiple filters** 253 **Example 2. Using multiple filters**
257 254
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. 255 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): 256 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):
260 257
261 .. image:: ${static_path}/images/multiple-filters.png 258 .. image:: images/multiple-filters.png
262 259
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. 260 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. 261 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.
265 262
266 ----- 263 -----
269 266
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*) 267 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*. 268 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: 269 The following screenshot expalins how this can be done:
273 270
274 .. image:: ${static_path}/images/complex-filters.png 271 .. image:: images/complex-filters.png
275 272
276 ----- 273 -----
277 274
278 **Example 4. Even more complex filtering with Rules** 275 **Example 4. Even more complex filtering with Rules**
279 276
283 280
284 !(1) &amp; (2 | 3) 281 !(1) &amp; (2 | 3)
285 282
286 Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy: 283 Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy:
287 284
288 .. image:: ${static_path}/images/rule.png 285 .. image:: images/rule.png
289 286
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. 287 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:: 288 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::
292 289
293 NOT condition 1 AND (condition 2 OR condition 3) 290 NOT condition 1 AND (condition 2 OR condition 3)
310 "tag":"NM:>0", 307 "tag":"NM:>0",
311 "isReverseStrand":"true" 308 "isReverseStrand":"true"
312 } 309 }
313 ] 310 ]
314 } 311 }
315 312
316
317 313
318 ----- 314 -----
319 315
320 **More information** 316 **More information**
321 317