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comparison bamtools.xml @ 0:2c2200cecea2 draft

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author anton
date Wed, 10 Sep 2014 11:55:26 -0400
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1 <?xml version="1.0"?>
2 <tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.1">
3 <description>BAM datasets and perform other transformations</description>
4 <requirements>
5 <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>
6 <requirement type="package" version="0.1.18">samtools</requirement>
7 </requirements>
8
9 <command>
10 ##set up input files
11
12 #for $bam_count, $input_bam in enumerate( $input_bams ):
13 ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
14 ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
15 #end for
16
17 #if str( $analysis_type.analysis_type_selector ) == "convert":
18 #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
19 #set $reference_fasta_filename = "localref.fa"
20 #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history":
21 ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
22 samtools faidx "${reference_fasta_filename}" 2&gt;&amp;1 || echo "Error running samtools faidx for bamtools convert" &gt;&amp;2 &amp;&amp;
23 #else:
24 #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )
25 #end if
26 #end if
27 #end if
28
29 ##finished setting up inputs
30
31 ##start bamtools commandline
32
33 bamtools
34
35 #if str( $analysis_type.analysis_type_selector ) == "convert":
36
37 convert
38
39 -format ${analysis_type.format_type.format_type_selector}
40
41 #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
42
43 ${analysis_type.format_type.mapqual}
44 -fasta "${reference_fasta_filename}"
45
46 #elif str( $analysis_type.format_type.format_type_selector ) == "sam":
47
48 ${analysis_type.format_type.noheader}
49
50 #end if
51
52 -out $out_file1
53
54 #elif str( $analysis_type.analysis_type_selector ) == "count":
55
56 count
57 > $out_file1
58
59 #elif str( $analysis_type.analysis_type_selector ) == "coverage":
60
61 coverage
62 -out $out_file1
63
64 #elif str( $analysis_type.analysis_type_selector ) == "header":
65
66 header
67 > $out_file1
68
69 #elif str( $analysis_type.analysis_type_selector ) == "merge":
70
71 merge
72 -out $out_file1
73
74 #elif str( $analysis_type.analysis_type_selector ) == "random":
75
76 random
77 -n ${analysis_type.count}
78 -seed ${analysis_type.seed}
79 -out $out_file1
80
81 #elif str( $analysis_type.analysis_type_selector ) == "revert":
82
83 revert
84 ${analysis_type.keepDuplicate}
85 ${analysis_type.keepQualities}
86 -out $out_file1
87
88 #elif str( $analysis_type.analysis_type_selector ) == "sort":
89
90 sort
91 ${analysis_type.byname}
92 -out $out_file1
93
94 #end if
95
96 #for $bam_count, $input_bam in enumerate( $input_bams ):
97 -in "localbam_${bam_count}.bam"
98 #end for
99
100
101 </command>
102 <inputs>
103
104 <repeat name="input_bams" title="BAM dataset(s) to filter" min="1">
105 <param name="input_bam" type="data" format="bam" label="BAM dataset" />
106 </repeat>
107
108 <conditional name="analysis_type">
109 <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">
110 <option value="convert">Convert</option>
111 <option value="count">Count</option>
112 <option value="coverage">Coverage</option>
113 <option value="header">Header</option>
114 <option value="merge">Merge</option>
115 <option value="random">Random</option>
116 <option value="revert">Revert</option>
117 <!-- The sort option below is commented out as BAM files in Galaxy as reference sorted by dafault. -->
118 <!-- Allowing users for sort files may break donstream functionality. -->
119 <!-- To enable sort option simply uncomment the line below: -->
120 <!-- <option value="sort">Sort</option> -->
121 </param>
122 <when value="convert">
123 <conditional name="format_type">
124 <param name="format_type_selector" type="select" help="Select what to convert your BAM to">
125 <option value="bed">BED</option>
126 <option value="fasta">FASTA</option>
127 <option value="fastq">FASTQ</option>
128 <option value="json">JSON</option>
129 <option value="pileup">Pileup</option>
130 <option value="sam">SAM</option>
131 <option value="yaml">YAML</option>
132 </param>
133 <when value="pileup">
134 <conditional name="reference_source">
135 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
136 <option value="cached">Locally cached</option>
137 <option value="history">History</option>
138 </param>
139 <when value="cached">
140 <param name="ref_file" type="select" label="Using reference genome">
141 <options from_data_table="sam_fa_indexes">
142 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
143 </options>
144 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
145 </param>
146 </when>
147 <when value="history"> <!-- FIX ME!!!! -->
148 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
149 </when>
150 </conditional>
151 <param name="mapqual" type="boolean" truevalue="-mapqual" falsevalue="" label="Print quality scores?" />
152 </when>
153 <when value="sam">
154 <param name="noheader" type="boolean" truevalue="-noheader" falsevalue="" label="Do not print header" />
155 </when>
156 </conditional>
157 </when>
158 <when value="count">
159 <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
160 </when>
161 <when value="coverage">
162 <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
163 </when>
164 <when value="header">
165 <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
166 </when>
167 <when value="merge">
168 <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
169 </when>
170 <when value="random">
171 <param name="count" type="integer" value="10000" label="Number of random alignments to grab" help="No duplicate checking is perfomed" />
172 <param name="seed" type="integer" value="1024" label="Random number generator seed" help="Use the same seed for reproducible results" />
173 </when>
174 <when value="revert">
175 <param name="keepDuplicate" type="boolean" truevalue="-keepDuplicate" falsevalue="" label="Keep duplicates marked" help="Do not remove duplicate marks" />
176 <param name="keepQualities" type="boolean" truevalue="-keepQualities" falsevalue="" label="Keep base qualities" help="Do not replace qualities with contect of OQ tag" />
177 </when>
178 <when value="sort">
179 <param name="byname" type="boolean" truevalue="-byname" falsevalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/>
180 </when>
181 </conditional>
182
183 </inputs>
184 <outputs>
185 <data format="txt" name="out_file1">
186 <change_format>
187 <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" />
188 <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" />
189 <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" />
190 <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" />
191 <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" />
192 <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" />
193 <when input="analysis_type.analysis_type_selector" value="merge" format="bam" />
194 <when input="analysis_type.analysis_type_selector" value="random" format="bam" />
195 <when input="analysis_type.analysis_type_selector" value="revert" format="bam" />
196 <when input="analysis_type.analysis_type_selector" value="sort" format="bam" />
197 </change_format>
198 </data>
199 </outputs>
200 <tests>
201 <test>
202 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
203 <param name="analysis_type_selector" value="convert"/>
204 <param name="format_type_selector" value="pileup"/>
205 <param name="reference_source_selector" value="history" />
206 <param name="mapqual" value="true" />
207 <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>
208 <output name="output_bam" file="bamtools-convert-pileup.pu" />
209 </test>
210 <test>
211 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
212 <param name="analysis_type_selector" value="count"/>
213 <output name="output_bam" file="bamtools-count.tab" />
214 </test>
215 <test>
216 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
217 <param name="analysis_type_selector" value="coverage"/>
218 <output name="output_bam" file="bamtools-coverage.tab" />
219 </test>
220 <test>
221 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
222 <param name="analysis_type_selector" value="header"/>
223 <output name="output_bam" file="bamtools-header.txt" />
224 </test>
225 </tests>
226
227 <stdio>
228 <exit_code range="1:" />
229 </stdio>
230
231 <help>
232
233 **What is does**
234
235 BAMTools is a collection of utilities for manipulation on BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
236 This Galaxy implementation of BAMTools utilities includes seven utilities - Convert, Count, Coverage, Header, Merge, Random, and Revert - decsribed in detail below.
237
238 -----
239
240 **Convert**
241
242 Converts BAM dataset(s) into BED, FASTA, FASTQ, JSON, Pileup, SAM, or YAML formats. Note that the conversion to the pileup format requires providing a reference sequence either
243 cashed at this Galaxy instance, or provided by you as a FASTA dataset from History.
244
245 -----
246
247 **Count**
248
249 Counts a number of alignments in a BAM dataset(s).
250
251 -----
252
253 **Coverage**
254
255 Prints per-base coverage for a BAM dataset.
256
257 -----
258
259 **Header**
260
261 Prints header from a BAM dataset(s).
262
263 ------
264
265 **Merge**
266
267 Merges multiple BAM datasets into a single one. Obviously, you need to select multiple BAMs as input, which is done by pressing the "**Add new BAM dataset(s) to filter**" button.
268
269 ------
270
271 **Random**
272
273 Grabs a specified number of random lines from BAM dataset(s).
274
275 ------
276
277 **Revert**
278
279 Removes duplicate marks and restores original (non-recalibrated) base qualities.
280
281 -----
282
283 .. class:: infomark
284
285 **More information**
286
287 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
288
289 </help>
290 </tool>