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comparison picard_FastqToSam.xml @ 8:e417b1d6288d draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:26 -0500
parents 08f69add4d06
children 486d7500da69
comparison
equal deleted inserted replaced
7:08f69add4d06 8:e417b1d6288d
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9
10 picard 9 picard
11 FastqToSam 10 FastqToSam
12 11
13 #if str( $input_type.input_type_selector ) == "se": 12 #if str( $input_type.input_type_selector ) == "se":
14 FASTQ="${input_type.fastq}" 13 FASTQ="${input_type.fastq}"
15 #elif str( $input_type.input_type_selector ) == "pe": 14 #elif str( $input_type.input_type_selector ) == "pe":
16 FASTQ="${input_type.fastq}" 15 FASTQ="${input_type.fastq}"
17 FASTQ2="${input_type.fastq2}" 16 FASTQ2="${input_type.fastq2}"
18 #else 17 #else
19 FASTQ="${input_type.fastq.forward}" 18 FASTQ="${input_type.fastq.forward}"
20 FASTQ2="${input_type.fastq.reverse}" 19 FASTQ2="${input_type.fastq.reverse}"
21 #end if 20 #end if
22 21
23 QUALITY_FORMAT="${quality_format}" 22 QUALITY_FORMAT="${quality_format}"
24 OUTPUT="${outFile}" 23 OUTPUT="${outFile}"
25 READ_GROUP_NAME="${read_group_name}" 24 READ_GROUP_NAME="${read_group_name}"
26 SAMPLE_NAME="${sample_name}" 25 SAMPLE_NAME="${sample_name}"
27 26
28 #if str( $library_name ): 27 #if str( $library_name ):
29 LIBRARY_NAME="${library_name}" 28 LIBRARY_NAME="${library_name}"
30 #end if 29 #end if
31 30
32 #if str( $platform_unit ): 31 #if str( $platform_unit ):
33 PLATFORM_UNIT="${platform_unit}" 32 PLATFORM_UNIT="${platform_unit}"
34 #end if 33 #end if
35 34
36 #if str( $platform ): 35 #if str( $platform ):
37 PLATFORM="${platform}" 36 PLATFORM="${platform}"
38 #end if 37 #end if
39 38
40 #if str( $sequencing_center ): 39 #if str( $sequencing_center ):
41 SEQUENCING_CENTER="${sequencing_center}" 40 SEQUENCING_CENTER="${sequencing_center}"
42 #end if 41 #end if
43 42
44 #if str( $predicted_insert_size ): 43 #if str( $predicted_insert_size ):
45 PREDICTED_INSERT_SIZE="${predicted_insert_size}" 44 PREDICTED_INSERT_SIZE="${predicted_insert_size}"
46 #end if 45 #end if
47 46
48 #if str( $comment ): 47 #if str( $comment ):
49 COMMENT="${comment}" 48 COMMENT="${comment}"
50 #end if 49 #end if
51 50
52 #if str( $description ): 51 #if str( $description ):
53 DESCRIPTION="${description}" 52 DESCRIPTION="${description}"
54 #end if 53 #end if
55 54
56 #if str( $run_date ): 55 #if str( $run_date ):
57 RUN_DATE="${run_date}" 56 RUN_DATE="${run_date}"
58 #end if 57 #end if
59 58
60 MIN_Q="${min_q}" 59 MIN_Q="${min_q}"
61 MAX_Q="${max_q}" 60 MAX_Q="${max_q}"
62 STRIP_UNPAIRED_MATE_NUMBER="${strip_unpairied_mate_number}" 61 STRIP_UNPAIRED_MATE_NUMBER="${strip_unpairied_mate_number}"
63 ALLOW_AND_IGNORE_EMPTY_LINES="${allow_and_ignore_empty_lines}" 62 ALLOW_AND_IGNORE_EMPTY_LINES="${allow_and_ignore_empty_lines}"
64 63
65 SORT_ORDER=coordinate 64 SORT_ORDER=coordinate
66 VALIDATION_STRINGENCY="${validation_stringency}" 65 VALIDATION_STRINGENCY="${validation_stringency}"
67 QUIET=true 66 QUIET=true
68 VERBOSITY=ERROR 67 VERBOSITY=ERROR
69 68
70 ]]></command> 69 ]]></command>
71 <inputs> 70 <inputs>
72 <conditional name="input_type"> 71 <conditional name="input_type">
73 <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"> 72 <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">
74 <option value="se">Single end (single dataset)</option> 73 <option value="se">Single end (single dataset)</option>
84 </when> 83 </when>
85 <when value="pc"> 84 <when value="pc">
86 <param name="fastq" type="data_collection" collection_type="paired" format="fastq" 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"/> 85 <param name="fastq" type="data_collection" collection_type="paired" format="fastq" 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"/>
87 </when> 86 </when>
88 </conditional> 87 </conditional>
89 88
90 <param name="quality_format" type="select" label="Select quality encoding scheme" help="QUALITY_FORMAT"> 89 <param name="quality_format" type="select" label="Select quality encoding scheme" help="QUALITY_FORMAT">
91 <option value="Standard" selected="True">Sanger (+33)</option> 90 <option value="Standard" selected="True">Sanger (+33)</option>
92 <option value="Illumina">Illumina (+64)</option> 91 <option value="Illumina">Illumina (+64)</option>
93 <option value="Solexa">Solexa (+66)</option> 92 <option value="Solexa">Solexa (+66)</option>
94 </param> 93 </param>
106 <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/> 105 <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
107 <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"/> 106 <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"/>
108 <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"/> 107 <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"/>
109 <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"/> 108 <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"/>
110 <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"/> 109 <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"/>
111 110
112 <expand macro="VS" /> 111 <expand macro="VS" />
113 112
114 </inputs> 113 </inputs>
115 114
116 <outputs> 115 <outputs>
117 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/> 116 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/>
118 </outputs> 117 </outputs>
119 118
120 <tests> 119 <tests>
121 <test> 120 <test>
122 <param name="input_type_selector" value="pe" /> 121 <param name="input_type_selector" value="pe" />
123 <param name="quality_format" value="Standard" /> 122 <param name="quality_format" value="Standard" />
124 <param name="read_group_name" value="A" /> 123 <param name="read_group_name" value="A" />
137 <param name="allow_and_ignore_empty_lines" value="False" /> 136 <param name="allow_and_ignore_empty_lines" value="False" />
138 <param name="validation_stringency" value="LENIENT"/> 137 <param name="validation_stringency" value="LENIENT"/>
139 <param name="fastq" value="picard_FastqToSam_read1.fq" ftype="fastq" /> 138 <param name="fastq" value="picard_FastqToSam_read1.fq" ftype="fastq" />
140 <param name="fastq2" value="picard_FastqToSam_read2.fq" ftype="fastq" /> 139 <param name="fastq2" value="picard_FastqToSam_read2.fq" ftype="fastq" />
141 <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="bam" lines_diff="4"/> 140 <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="bam" lines_diff="4"/>
142 </test> 141 </test>
143 </tests> 142 </tests>
144 143
145 <help> 144 <help>
146 145
147 .. class:: infomark 146 .. class:: infomark
148 147
149 **Purpose** 148 **Purpose**
155 @RG@ 154 @RG@
156 155
157 @description@ 156 @description@
158 157
159 FASTQ=File 158 FASTQ=File
160 F1=File Input fastq file for single end data, or first read in paired end 159 F1=File Input fastq file for single end data, or first read in paired end
161 data. Required. 160 data. Required.
162 161
163 FASTQ2=File 162 FASTQ2=File
164 F2=File Input fastq file for the second read of paired end data (if used). 163 F2=File Input fastq file for the second read of paired end data (if used).
165 164
166 QUALITY_FORMAT=FastqQualityFormat 165 QUALITY_FORMAT=FastqQualityFormat
167 V=FastqQualityFormat A value describing how the quality values are encoded in the fastq. Either Solexa for 166 V=FastqQualityFormat A value describing how the quality values are encoded in the fastq. Either Solexa for
168 pre-pipeline 1.3 style scores (solexa scaling + 66), Illumina for pipeline 1.3 and above 167 pre-pipeline 1.3 style scores (solexa scaling + 66), Illumina for pipeline 1.3 and above
169 (phred scaling + 64) or Standard for phred scaled scores with a character shift of 33. 168 (phred scaling + 64) or Standard for phred scaled scores with a character shift of 33.
170 If this value is not specified, the quality format will be detected automatically. 169 If this value is not specified, the quality format will be detected automatically.
171 Default value: null. Possible values: {Solexa, Illumina, Standard} 170 Default value: null. Possible values: {Solexa, Illumina, Standard}
172 171
173 READ_GROUP_NAME=String 172 READ_GROUP_NAME=String
174 RG=String Read group name Default value: A. 173 RG=String Read group name Default value: A.
175 174
176 SAMPLE_NAME=String 175 SAMPLE_NAME=String
177 SM=String Sample name to insert into the read group header Required. 176 SM=String Sample name to insert into the read group header Required.
178 177
179 LIBRARY_NAME=String 178 LIBRARY_NAME=String
180 LB=String The library name to place into the LB attribute in the read group header. 179 LB=String The library name to place into the LB attribute in the read group header.
181 180
182 PLATFORM_UNIT=String 181 PLATFORM_UNIT=String
183 PU=String The platform unit (often run_barcode.lane) to insert into the read group header. 182 PU=String The platform unit (often run_barcode.lane) to insert into the read group header.
184 183
185 PLATFORM=String 184 PLATFORM=String
186 PL=String The platform type (e.g. illumina, solid) to insert into the read group header. 185 PL=String The platform type (e.g. illumina, solid) to insert into the read group header.
187 186
188 SEQUENCING_CENTER=String 187 SEQUENCING_CENTER=String
189 CN=String The sequencing center from which the data originated. 188 CN=String The sequencing center from which the data originated.
190 189
191 PREDICTED_INSERT_SIZE=Integer 190 PREDICTED_INSERT_SIZE=Integer
192 PI=Integer Predicted median insert size, to insert into the read group header. 191 PI=Integer Predicted median insert size, to insert into the read group header.
193 192
194 COMMENT=String 193 COMMENT=String
195 CO=String Comment to include in the merged output file's header. 194 CO=String Comment to include in the merged output file's header.
196 195
197 DESCRIPTION=String 196 DESCRIPTION=String
198 DS=String Inserted into the read group header. 197 DS=String Inserted into the read group header.
199 198
200 RUN_DATE=Iso8601Date 199 RUN_DATE=Iso8601Date
201 DT=Iso8601Date Date the run was produced, to insert into the read group header. 200 DT=Iso8601Date Date the run was produced, to insert into the read group header.
202 201
203 MIN_Q=Integer Minimum quality allowed in the input fastq. An exception will be thrown if a quality is 202 MIN_Q=Integer Minimum quality allowed in the input fastq. An exception will be thrown if a quality is
204 less than this value. Default value: 0. 203 less than this value. Default value: 0.
205 204
206 MAX_Q=Integer Maximum quality allowed in the input fastq. An exception will be thrown if a quality is 205 MAX_Q=Integer Maximum quality allowed in the input fastq. An exception will be thrown if a quality is
207 greater than this value. Default value: 93. 206 greater than this value. Default value: 93.
208 207
209 STRIP_UNPAIRED_MATE_NUMBER=Boolean 208 STRIP_UNPAIRED_MATE_NUMBER=Boolean
210 If true and this is an unpaired fastq any occurance of '/1' will be removed from the end 209 If true and this is an unpaired fastq any occurance of '/1' will be removed from the end
211 of a read name. Default value: false. Possible values: {true, false} 210 of a read name. Default value: false. Possible values: {true, false}
212 211
213 ALLOW_AND_IGNORE_EMPTY_LINES=Boolean 212 ALLOW_AND_IGNORE_EMPTY_LINES=Boolean
214 Allow (and ignore) empty lines Default value: false. Possible values: {true, false} 213 Allow (and ignore) empty lines Default value: false. Possible values: {true, false}
215 214
216 215
217 @more_info@ 216 @more_info@
218 217
219 </help> 218 </help>
220 <citations> 219 <citations>