Mercurial > repos > devteam > picard_plus
comparison picard_FastqToSam.xml @ 0:4419e9980172 draft
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author | devteam |
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date | Thu, 23 Oct 2014 12:03:34 -0400 |
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1 <tool name="FastqToSam" id="picard_FastqToSam" version="1.122.0"> | |
2 <description>convert Fastq data into unaligned BAM</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.122.0">picard</requirement> | |
5 </requirements> | |
6 | |
7 <macros> | |
8 <import>picard_macros.xml</import> | |
9 </macros> | |
10 | |
11 <command> | |
12 @java_options@ | |
13 | |
14 java -jar \$JAVA_JAR_PATH/FastqToSam.jar | |
15 | |
16 #if str( $input_type.input_type_selector ) == "se": | |
17 FASTQ="${input_type.fastq}" | |
18 #elif str( $input_type.input_type_selector ) == "pe": | |
19 FASTQ="${input_type.fastq}" | |
20 FASTQ2="${input_type.fastq2}" | |
21 #else | |
22 FASTQ="${input_type.fastq.forward}" | |
23 FASTQ2="${input_type.fastq.reverse}" | |
24 #end if | |
25 | |
26 QUALITY_FORMAT="${quality_format}" | |
27 OUTPUT="${outFile}" | |
28 READ_GROUP_NAME="${read_group_name}" | |
29 SAMPLE_NAME="${sample_name}" | |
30 | |
31 #if str( $library_name ): | |
32 LIBRARY_NAME="${library_name}" | |
33 #end if | |
34 | |
35 #if str( $platform_unit ): | |
36 PLATFORM_UNIT="${platform_unit}" | |
37 #end if | |
38 | |
39 #if str( $platform ): | |
40 PLATFORM="${platform}" | |
41 #end if | |
42 | |
43 #if str( $sequencing_center ): | |
44 SEQUENCING_CENTER="${sequencing_center}" | |
45 #end if | |
46 | |
47 #if str( $predicted_insert_size ): | |
48 PREDICTED_INSERT_SIZE="${predicted_insert_size}" | |
49 #end if | |
50 | |
51 #if str( $comment ): | |
52 COMMENT="${comment}" | |
53 #end if | |
54 | |
55 #if str( $description ): | |
56 DESCRIPTION="${description}" | |
57 #end if | |
58 | |
59 #if str( $run_date ): | |
60 RUN_DATE="${run_date}" | |
61 #end if | |
62 | |
63 MIN_Q="${min_q}" | |
64 MAX_Q="${max_q}" | |
65 STRIP_UNPAIRED_MATE_NUMBER="${strip_unpairied_mate_number}" | |
66 ALLOW_AND_IGNORE_EMPTY_LINES="${allow_and_ignore_empty_lines}" | |
67 | |
68 SORT_ORDER=coordinate | |
69 VALIDATION_STRINGENCY="${validation_stringency}" | |
70 QUIET=true | |
71 VERBOSITY=ERROR | |
72 | |
73 </command> | |
74 <inputs> | |
75 <conditional name="input_type"> | |
76 <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types"> | |
77 <option value="se">Single end (single dataset)</option> | |
78 <option value="pe">Paired end (two datasets)</option> | |
79 <option value="pc">Paired collection</option> | |
80 </param> | |
81 <when value="se"> | |
82 <param name="fastq" type="data" format="fastq" label="Input fastq file for single end data" help="FASTQ"/> | |
83 </when> | |
84 <when value="pe"> | |
85 <param name="fastq" type="data" format="fastq" label="Input fastq file for the first read in paired end data" help="FASTQ"/> | |
86 <param name="fastq2" type="data" format="fastq" label="Input fastq file for the second read of paired end data" help="FASTQ2"/> | |
87 </when> | |
88 <when value="pc"> | |
89 <param name="fastq" type="data_collection" collection_type="paired" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/> | |
90 </when> | |
91 </conditional> | |
92 | |
93 <param name="quality_format" type="select" label="Select quality encoding scheme" help="QUALITY_FORMAT"> | |
94 <option value="Standard" selected="True">Sanger (+33)</option> | |
95 <option value="Illumina">Illumina (+64)</option> | |
96 <option value="Solexa">Solexa (+66)</option> | |
97 </param> | |
98 | |
99 <param name="read_group_name" type="text" size="20" value="A" label="Read group name" help="READ_GROUP_NAME"/> | |
100 <param name="sample_name" type="text" size="20" value="sample-a" label="Sample name" help="SAMPLE_NAME"/> | |
101 <param name="library_name" type="text" size="20" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/> | |
102 <param name="platform_unit" type="text" size="20" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/> | |
103 <param name="platform" type="text" size="20" optional="True" label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/> | |
104 <param name="sequencing_center" type="text" size="20" optional="True" label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/> | |
105 | |
106 <param name="predicted_insert_size" type="integer" min="0" max="100000" optional="True" label="Predicted median insert size, to insert into the read group header" help="PREDICTED_INSERT_SIZE; Optional"/> | |
107 <param name="comment" type="text" size="20" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/> | |
108 <param name="description" type="text" size="20" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/> | |
109 <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/> | |
110 <param name="min_q" type="integer" value="0" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MIN_Q; An exception will be thrown if a quality is less than this value; default=0"/> | |
111 <param name="max_q" type="integer" value="93" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MAX_Q; An exception will be thrown if a quality is greater than this value; default=93"/> | |
112 <param name="strip_unpairied_mate_number" type="boolean" truevalue="true" falsevalue="false" label="If true and this is an unpaired fastq any occurance of '/1' will be removed from the end of a read name" help="STRIP_UNPAIRED_MATE_NUMBER; default=false"/> | |
113 <param name="allow_and_ignore_empty_lines" type="boolean" truevalue="true" falsevalue="false" label="Allow (and ignore) empty lines" help="ALLOW_AND_IGNORE_EMPTY_LINES; default=false"/> | |
114 | |
115 <expand macro="VS" /> | |
116 | |
117 </inputs> | |
118 | |
119 <outputs> | |
120 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/> | |
121 </outputs> | |
122 | |
123 <tests> | |
124 <test> | |
125 <param name="input_type_selector" value="pe" /> | |
126 <param name="quality_format" value="Standard" /> | |
127 <param name="read_group_name" value="A" /> | |
128 <param name="sample_name" value="sample-a" /> | |
129 <param name="library_name" value="A"/> | |
130 <param name="platform_unit" value="A"/> | |
131 <param name="platform" value="Illumina"/> | |
132 <param name="sequencing_center" value="A"/> | |
133 <param name="predicted_insert_size" value="300"/> | |
134 <param name="comment" value="A"/> | |
135 <param name="description" value="A"/> | |
136 <param name="run_date" value="2014-10-10"/> | |
137 <param name="min_q" value="0" /> | |
138 <param name="max_q" value="93" /> | |
139 <param name="strip_unpairied_mate_number" value="False" /> | |
140 <param name="allow_and_ignore_empty_lines" value="False" /> | |
141 <param name="validation_stringency" value="LENIENT"/> | |
142 <param name="fastq" value="picard_FastqToSam_read1.fq" ftype="fastq" /> | |
143 <param name="fastq2" value="picard_FastqToSam_read2.fq" ftype="fastq" /> | |
144 <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="bam" lines_diff="4"/> | |
145 </test> | |
146 </tests> | |
147 | |
148 <stdio> | |
149 <exit_code range="1:" level="fatal"/> | |
150 </stdio> | |
151 | |
152 <help> | |
153 | |
154 .. class:: infomark | |
155 | |
156 **Purpose** | |
157 | |
158 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. | |
159 | |
160 @dataset_collections@ | |
161 | |
162 @RG@ | |
163 | |
164 @description@ | |
165 | |
166 FASTQ=File | |
167 F1=File Input fastq file for single end data, or first read in paired end | |
168 data. Required. | |
169 | |
170 FASTQ2=File | |
171 F2=File Input fastq file for the second read of paired end data (if used). | |
172 | |
173 QUALITY_FORMAT=FastqQualityFormat | |
174 V=FastqQualityFormat A value describing how the quality values are encoded in the fastq. Either Solexa for | |
175 pre-pipeline 1.3 style scores (solexa scaling + 66), Illumina for pipeline 1.3 and above | |
176 (phred scaling + 64) or Standard for phred scaled scores with a character shift of 33. | |
177 If this value is not specified, the quality format will be detected automatically. | |
178 Default value: null. Possible values: {Solexa, Illumina, Standard} | |
179 | |
180 READ_GROUP_NAME=String | |
181 RG=String Read group name Default value: A. | |
182 | |
183 SAMPLE_NAME=String | |
184 SM=String Sample name to insert into the read group header Required. | |
185 | |
186 LIBRARY_NAME=String | |
187 LB=String The library name to place into the LB attribute in the read group header. | |
188 | |
189 PLATFORM_UNIT=String | |
190 PU=String The platform unit (often run_barcode.lane) to insert into the read group header. | |
191 | |
192 PLATFORM=String | |
193 PL=String The platform type (e.g. illumina, solid) to insert into the read group header. | |
194 | |
195 SEQUENCING_CENTER=String | |
196 CN=String The sequencing center from which the data originated. | |
197 | |
198 PREDICTED_INSERT_SIZE=Integer | |
199 PI=Integer Predicted median insert size, to insert into the read group header. | |
200 | |
201 COMMENT=String | |
202 CO=String Comment to include in the merged output file's header. | |
203 | |
204 DESCRIPTION=String | |
205 DS=String Inserted into the read group header. | |
206 | |
207 RUN_DATE=Iso8601Date | |
208 DT=Iso8601Date Date the run was produced, to insert into the read group header. | |
209 | |
210 MIN_Q=Integer Minimum quality allowed in the input fastq. An exception will be thrown if a quality is | |
211 less than this value. Default value: 0. | |
212 | |
213 MAX_Q=Integer Maximum quality allowed in the input fastq. An exception will be thrown if a quality is | |
214 greater than this value. Default value: 93. | |
215 | |
216 STRIP_UNPAIRED_MATE_NUMBER=Boolean | |
217 If true and this is an unpaired fastq any occurance of '/1' will be removed from the end | |
218 of a read name. Default value: false. Possible values: {true, false} | |
219 | |
220 ALLOW_AND_IGNORE_EMPTY_LINES=Boolean | |
221 Allow (and ignore) empty lines Default value: false. Possible values: {true, false} | |
222 | |
223 | |
224 @more_info@ | |
225 | |
226 </help> | |
227 </tool> | |
228 | |
229 |