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comparison bamtools.xml @ 2:ea3fc1adee75 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:33:26 -0500
parents 76b2f1eee508
children 04866f817daa
comparison
equal deleted inserted replaced
1:c1a1bea37098 2:ea3fc1adee75
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.1"> 2 <tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.2">
3 <description>BAM datasets and perform other transformations</description> 3 <description>BAM datasets and perform other transformations</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement> 5 <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>
6 <requirement type="package" version="0.1.18">samtools</requirement> 6 <requirement type="package" version="0.1.18">samtools</requirement>
7 </requirements> 7 </requirements>
8 8
9 <command> 9 <command>
10 ##set up input files 10 ##set up input files
11 11
12 #for $bam_count, $input_bam in enumerate( $input_bams ): 12 #for $bam_count, $input_bam in enumerate( $input_bams ):
13 ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp; 13 ln -s "${input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
14 ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp; 14 ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
15 #end for 15 #end for
16 16
17 #if str( $analysis_type.analysis_type_selector ) == "convert": 17 #if str( $analysis_type.analysis_type_selector ) == "convert":
18 #if str( $analysis_type.format_type.format_type_selector ) == "pileup": 18 #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
19 #set $reference_fasta_filename = "localref.fa" 19 #set $reference_fasta_filename = "localref.fa"
20 #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history": 20 #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history":
21 ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp; 21 ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
25 #end if 25 #end if
26 #end if 26 #end if
27 #end if 27 #end if
28 28
29 ##finished setting up inputs 29 ##finished setting up inputs
30 30
31 ##start bamtools commandline 31 ##start bamtools commandline
32 32
33 bamtools 33 bamtools
34 34
35 #if str( $analysis_type.analysis_type_selector ) == "convert": 35 #if str( $analysis_type.analysis_type_selector ) == "convert":
36 36
37 convert 37 convert
38 38
39 -format ${analysis_type.format_type.format_type_selector} 39 -format ${analysis_type.format_type.format_type_selector}
40 40
41 #if str( $analysis_type.format_type.format_type_selector ) == "pileup": 41 #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
42 42
43 ${analysis_type.format_type.mapqual} 43 ${analysis_type.format_type.mapqual}
44 -fasta "${reference_fasta_filename}" 44 -fasta "${reference_fasta_filename}"
45 45
46 #elif str( $analysis_type.format_type.format_type_selector ) == "sam": 46 #elif str( $analysis_type.format_type.format_type_selector ) == "sam":
47 47
48 ${analysis_type.format_type.noheader} 48 ${analysis_type.format_type.noheader}
49 49
50 #end if 50 #end if
51 51
52 -out $out_file1 52 -out $out_file1
53 53
54 #elif str( $analysis_type.analysis_type_selector ) == "count": 54 #elif str( $analysis_type.analysis_type_selector ) == "count":
55 55
56 count 56 count
57 > $out_file1 57 > $out_file1
58 58
59 #elif str( $analysis_type.analysis_type_selector ) == "coverage": 59 #elif str( $analysis_type.analysis_type_selector ) == "coverage":
60 60
61 coverage 61 coverage
62 -out $out_file1 62 -out $out_file1
63 63
64 #elif str( $analysis_type.analysis_type_selector ) == "header": 64 #elif str( $analysis_type.analysis_type_selector ) == "header":
65 65
66 header 66 header
67 > $out_file1 67 > $out_file1
68 68
69 #elif str( $analysis_type.analysis_type_selector ) == "merge": 69 #elif str( $analysis_type.analysis_type_selector ) == "merge":
70 70
71 merge 71 merge
72 -out $out_file1 72 -out $out_file1
73 73
74 #elif str( $analysis_type.analysis_type_selector ) == "random": 74 #elif str( $analysis_type.analysis_type_selector ) == "random":
75 75
76 random 76 random
77 -n ${analysis_type.count} 77 -n ${analysis_type.count}
78 -seed ${analysis_type.seed} 78 -seed ${analysis_type.seed}
79 -out $out_file1 79 -out $out_file1
80 80
81 #elif str( $analysis_type.analysis_type_selector ) == "revert": 81 #elif str( $analysis_type.analysis_type_selector ) == "revert":
82 82
83 revert 83 revert
84 ${analysis_type.keepDuplicate} 84 ${analysis_type.keepDuplicate}
85 ${analysis_type.keepQualities} 85 ${analysis_type.keepQualities}
86 -out $out_file1 86 -out $out_file1
87 87
88 #elif str( $analysis_type.analysis_type_selector ) == "sort": 88 #elif str( $analysis_type.analysis_type_selector ) == "sort":
89 89
90 sort 90 sort
91 ${analysis_type.byname} 91 ${analysis_type.byname}
92 -out $out_file1 92 -out $out_file1
93 93
94 #end if 94 #end if
95 95
96 #for $bam_count, $input_bam in enumerate( $input_bams ): 96 #for $bam_count, $input_bam in enumerate( $input_bams ):
97 -in "localbam_${bam_count}.bam" 97 -in "localbam_${bam_count}.bam"
98 #end for 98 #end for
99 99
100 100
101 </command> 101 </command>
102 <inputs> 102 <inputs>
103 103
104 <repeat name="input_bams" title="BAM dataset(s) to filter" min="1"> 104 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
105 <param name="input_bam" type="data" format="bam" label="BAM dataset" />
106 </repeat>
107 105
108 <conditional name="analysis_type"> 106 <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"> 107 <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> 108 <option value="convert">Convert</option>
111 <option value="count">Count</option> 109 <option value="count">Count</option>
177 </when> 175 </when>
178 <when value="sort"> 176 <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"/> 177 <param name="byname" type="boolean" truevalue="-byname" falsevalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/>
180 </when> 178 </when>
181 </conditional> 179 </conditional>
182 180
183 </inputs> 181 </inputs>
184 <outputs> 182 <outputs>
185 <data format="txt" name="out_file1"> 183 <data format="txt" name="out_file1">
186 <change_format> 184 <change_format>
187 <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" /> 185 <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" />
193 <when input="analysis_type.analysis_type_selector" value="merge" format="bam" /> 191 <when input="analysis_type.analysis_type_selector" value="merge" format="bam" />
194 <when input="analysis_type.analysis_type_selector" value="random" format="bam" /> 192 <when input="analysis_type.analysis_type_selector" value="random" format="bam" />
195 <when input="analysis_type.analysis_type_selector" value="revert" format="bam" /> 193 <when input="analysis_type.analysis_type_selector" value="revert" format="bam" />
196 <when input="analysis_type.analysis_type_selector" value="sort" format="bam" /> 194 <when input="analysis_type.analysis_type_selector" value="sort" format="bam" />
197 </change_format> 195 </change_format>
198 </data> 196 </data>
199 </outputs> 197 </outputs>
200 <tests> 198 <tests>
201 <test> 199 <test>
202 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> 200 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
203 <param name="analysis_type_selector" value="convert"/> 201 <param name="analysis_type_selector" value="convert"/>
204 <param name="format_type_selector" value="pileup"/> 202 <param name="format_type_selector" value="pileup"/>
205 <param name="reference_source_selector" value="history" /> 203 <param name="reference_source_selector" value="history" />
206 <param name="mapqual" value="true" /> 204 <param name="mapqual" value="true" />
207 <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/> 205 <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>
208 <output name="output_bam" file="bamtools-convert-pileup.pu" /> 206 <output name="output_bam" file="bamtools-convert-pileup.pu" />
209 </test> 207 </test>
210 <test> 208 <test>
211 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> 209 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
212 <param name="analysis_type_selector" value="count"/> 210 <param name="analysis_type_selector" value="count"/>
213 <output name="output_bam" file="bamtools-count.tab" /> 211 <output name="output_bam" file="bamtools-count.tab" />
214 </test> 212 </test>
215 <test> 213 <test>
216 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> 214 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
217 <param name="analysis_type_selector" value="coverage"/> 215 <param name="analysis_type_selector" value="coverage"/>
218 <output name="output_bam" file="bamtools-coverage.tab" /> 216 <output name="output_bam" file="bamtools-coverage.tab" />
219 </test> 217 </test>
220 <test> 218 <test>
221 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> 219 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
222 <param name="analysis_type_selector" value="header"/> 220 <param name="analysis_type_selector" value="header"/>
223 <output name="output_bam" file="bamtools-header.txt" /> 221 <output name="output_bam" file="bamtools-header.txt" />
224 </test> 222 </test>
225 </tests> 223 </tests>
226 224
227 <stdio> 225 <stdio>
228 <exit_code range="1:" /> 226 <exit_code range="1:" />
229 </stdio> 227 </stdio>
230 228
231 <help> 229 <help>
232 230
233 **What is does** 231 **What is does**
234 232
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). 233 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).