Mercurial > repos > devteam > picard_122_up
comparison picard_SamToFastq.xml @ 0:b76a4f17bbbb draft
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author | devteam |
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date | Thu, 23 Oct 2014 11:31:30 -0400 |
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-1:000000000000 | 0:b76a4f17bbbb |
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1 <tool name="SamToFastq" id="picard_SamToFastq" version="1.122.0"> | |
2 <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</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 | |
13 echo "BAM" > $report && ## This is necessary for output dataset detection (see output tags below) | |
14 | |
15 @java_options@ | |
16 | |
17 java -jar \$JAVA_JAR_PATH/SamToFastq.jar | |
18 | |
19 INPUT="${inputFile}" | |
20 | |
21 #if str( $output_per_rg ) == "true": | |
22 OUTPUT_PER_RG=true | |
23 OUTPUT_DIR=. | |
24 #elif str( $output_per_rg ) == "false" and str( $interleave ) == "false": | |
25 FASTQ=READ1.fastq | |
26 SECOND_END_FASTQ=READ2.fastq | |
27 UNPAIRED_FASTQ=UNPAIRED_READS.fastq | |
28 #elif str( $output_per_rg ) == "false" and str( $interleave ) == "true": | |
29 FASTQ=INTERLEAVED.fastq | |
30 #end if | |
31 | |
32 RE_REVERSE="${re_reverse}" | |
33 INTERLEAVE="${interleave}" | |
34 INCLUDE_NON_PF_READS="${include_non_pf_reads}" | |
35 CLIPPING_ATTRIBUTE="${clipping_attribute}" | |
36 CLIPPING_ACTION="${clipping_action}" | |
37 READ1_TRIM="${read1_trim}" | |
38 | |
39 #if int($read1_max_bases_to_write) > -1: | |
40 READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}" | |
41 #end if | |
42 | |
43 READ2_TRIM="${read2_trim}" | |
44 | |
45 #if int($read2_max_bases_to_write) > -1: | |
46 READ2_MAX_BASES_TO_WRITE="${read2_max_bases_to_write}" | |
47 #end if | |
48 | |
49 INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}" | |
50 | |
51 | |
52 VALIDATION_STRINGENCY="${validation_stringency}" | |
53 QUIET=true | |
54 VERBOSITY=ERROR | |
55 | |
56 </command> | |
57 <inputs> | |
58 | |
59 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> | |
60 <param name="output_per_rg" type="boolean" checked="False" label="Do you want to output a fastq file per read group (two fastq files per read group if the group is paired)" help="OUTPUT_PER_RG; default=False"/> | |
61 <param name="re_reverse" type="boolean" checked="True" label="Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq" help="RE_REVERSE; default=True"/> | |
62 <param name="interleave" type="boolean" label="Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe which end it came from" help="INTERLEAVE; default=False"/> | |
63 <param name="include_non_pf_reads" type="boolean" label="Include non-PF reads from the SAM/BAM dataset into the output FASTQ" help="INCLUDE_NON_PF_READS; PF means 'passes filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads; default=False"/> | |
64 <param name="clipping_attribute" type="text" size="4" value="null" label="The attribute that stores the position at which the SAM/BAM record should be clipped" help="CLIPPING_ATTRIBUTE; default=null"/> | |
65 <param name="clipping_action" type="text" size="10" value="null" label="The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region" help="CLIPPING_ACTION; default=null"/> | |
66 <param name="read1_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 1" help="READ1_TRIM; default=0"/> | |
67 <param name="read1_max_bases_to_write" type="integer" value="-1" label="The maximum number of bases to write from read 1 after trimming" help="READ1_MAX_BASES_TO_WRITE; If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written; default=null (-1)"/> | |
68 <param name="read2_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 2" help="READ2_TRIM; default=0"/> | |
69 <param name="read2_max_bases_to_write" type="integer" value="-1" label="The maximum number of bases to write from read 2 after trimming" help="READ2_MAX_BASES_TO_WRITE; If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written; default=null (-1)"/> | |
70 <param name="include_non_primary_alignments" type="boolean" label="If true, include non-primary alignments in the output" help="INCLUDE_NON_PRIMARY_ALIGNMENTS; Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments; default=False"/> | |
71 | |
72 <expand macro="VS" /> | |
73 | |
74 </inputs> | |
75 | |
76 <outputs> | |
77 <!-- here dataset discovery is based on fact that if OUTPUT_PER_RG=true this tool automatically adds .fastq extension to emitted files --> | |
78 <data format="txt" name="report" label="SamToFastq run" hidden="true"> | |
79 <discover_datasets pattern="(?P<designation>.+)\.fastq" ext="fastqsanger" visible="true"/> | |
80 </data> | |
81 </outputs> | |
82 | |
83 <tests> | |
84 <test> | |
85 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> | |
86 <param name="output_per_rg" value="false"/> | |
87 <param name="re_reverse" value="true"/> | |
88 <param name="interleave" value="true"/> | |
89 <param name="include_non_pf_reads" value="false"/> | |
90 <param name="clipping_attribute" value="null" /> | |
91 <param name="clipping_action" value="null" /> | |
92 <param name="read1_trim" value="0" /> | |
93 <param name="read1_max_bases_to_write" value="-1"/> | |
94 <param name="read2_trim" value="0" /> | |
95 <param name="read2_max_bases_to_write" value="-1"/> | |
96 <param name="include_non_primary_alignments" value="false"/> | |
97 <output name="report"> | |
98 <assert_contents> | |
99 <has_line line="BAM" /> | |
100 </assert_contents> | |
101 <discovered_dataset designation="INTERLEAVED" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/> | |
102 </output> | |
103 </test> | |
104 </tests> | |
105 | |
106 <stdio> | |
107 <exit_code range="1:" level="fatal"/> | |
108 </stdio> | |
109 | |
110 <help> | |
111 | |
112 **Purpose** | |
113 | |
114 Extracts read sequences and qualities from the input SAM/BAM dataset and outputs them in Sanger fastq format. In the RE_REVERSE=True mode (default behavior), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM.BAM dataset will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer. | |
115 | |
116 ----- | |
117 | |
118 .. class:: warningmark | |
119 | |
120 **DANGER: Multiple Outputs** | |
121 | |
122 Generating per readgroup fastq (setting **OUTPUT_PER_RG** to True) may produce very large numbers of outputs. Know what you are doing! | |
123 | |
124 @dataset_collections@ | |
125 | |
126 @description@ | |
127 | |
128 FASTQ=File | |
129 F=File Output fastq file (single-end fastq or, if paired, first end of the pair fastq). | |
130 Required. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG) | |
131 | |
132 SECOND_END_FASTQ=File | |
133 F2=File Output fastq file (if paired, second end of the pair fastq). Default value: null. | |
134 Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG) | |
135 | |
136 UNPAIRED_FASTQ=File | |
137 FU=File Output fastq file for unpaired reads; may only be provided in paired-fastq mode Default | |
138 value: null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG) | |
139 | |
140 OUTPUT_PER_RG=Boolean | |
141 OPRG=Boolean Output a fastq file per read group (two fastq files per read group if the group is | |
142 paired). Default value: false. Possible values: {true, false} Cannot be used in | |
143 conjuction with option(s) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) | |
144 | |
145 OUTPUT_DIR=File | |
146 ODIR=File Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true. | |
147 Default value: null. | |
148 | |
149 RE_REVERSE=Boolean | |
150 RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them | |
151 to fastq Default value: true. Possible values: {true, false} | |
152 | |
153 INTERLEAVE=Boolean | |
154 INTER=Boolean Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe | |
155 which end it came from Default value: false. Possible values: {true, false} | |
156 | |
157 INCLUDE_NON_PF_READS=Boolean | |
158 NON_PF=Boolean Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes | |
159 filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads. | |
160 Default value: false. Possible values: {true, false} | |
161 | |
162 CLIPPING_ATTRIBUTE=String | |
163 CLIP_ATTR=String The attribute that stores the position at which the SAM record should be clipped Default | |
164 value: null. | |
165 | |
166 CLIPPING_ACTION=String | |
167 CLIP_ACT=String The action that should be taken with clipped reads: 'X' means the reads and qualities | |
168 should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in | |
169 the clipped region; and any integer means that the base qualities should be set to that | |
170 value in the clipped region. Default value: null. | |
171 | |
172 READ1_TRIM=Integer | |
173 R1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0. | |
174 | |
175 READ1_MAX_BASES_TO_WRITE=Integer | |
176 R1_MAX_BASES=Integer The maximum number of bases to write from read 1 after trimming. If there are fewer than | |
177 this many bases left after trimming, all will be written. If this value is null then all | |
178 bases left after trimming will be written. Default value: null. | |
179 | |
180 READ2_TRIM=Integer | |
181 R2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0. | |
182 | |
183 READ2_MAX_BASES_TO_WRITE=Integer | |
184 R2_MAX_BASES=Integer The maximum number of bases to write from read 2 after trimming. If there are fewer than | |
185 this many bases left after trimming, all will be written. If this value is null then all | |
186 bases left after trimming will be written. Default value: null. | |
187 | |
188 INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean | |
189 If true, include non-primary alignments in the output. Support of non-primary alignments | |
190 in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and | |
191 there are paired reads with non-primary alignments. Default value: false. | |
192 Possible values: {true, false} | |
193 | |
194 @more_info@ | |
195 | |
196 </help> | |
197 </tool> | |
198 | |
199 |