Mercurial > repos > devteam > picard

annotate picard_FastqToSam.xml @ 28:881d7645d1bf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
author iuc
date Sat, 15 Jan 2022 12:39:30 +0000
parents 2a17c789e0a5
children 1aac2a13842a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 13
diff changeset
1 <tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
28
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
2 <description>convert Fastq data into unaligned BAM</description>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
3 <macros>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
4 <import>picard_macros.xml</import>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
5 <token name="@WRAPPER_VERSION@">1</token>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
6 </macros>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
7 <xrefs>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
8 <xref type="bio.tools">picard_fastqtosam</xref>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
9 </xrefs>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
10 <expand macro="requirements" />
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
12 @java_options@
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
13 picard
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
14 FastqToSam
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
15
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
16 #if str( $input_type.input_type_selector ) == "se":
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
17 FASTQ="${input_type.fastq}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
18 #elif str( $input_type.input_type_selector ) == "pe":
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
19 FASTQ="${input_type.fastq}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
20 FASTQ2="${input_type.fastq2}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
21 #else
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
22 FASTQ="${input_type.fastq.forward}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
23 FASTQ2="${input_type.fastq.reverse}"
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
24 #end if
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
25
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
26 QUALITY_FORMAT="${quality_format}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
27 OUTPUT="${outFile}"
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
28 READ_GROUP_NAME="${read_group_name}"
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
29 SAMPLE_NAME="${sample_name}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
30
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
31 #if str( $library_name ):
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
32 LIBRARY_NAME="${library_name}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
33 #end if
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
34
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
35 #if str( $platform_unit ):
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
36 PLATFORM_UNIT="${platform_unit}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
37 #end if
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
38
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
39 #if str( $platform ):
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
40 PLATFORM="${platform}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
41 #end if
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
42
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
43 #if str( $sequencing_center ):
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
44 SEQUENCING_CENTER="${sequencing_center}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
45 #end if
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
46
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
47 #if str( $predicted_insert_size ):
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
48 PREDICTED_INSERT_SIZE="${predicted_insert_size}"
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
49 #end if
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
50
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
51 #if str( $comment ):
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
52 COMMENT="${comment}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
53 #end if
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
54
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
55 #if str( $description ):
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
56 DESCRIPTION="${description}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
57 #end if
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
58
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
59 #if str( $run_date ):
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
60 RUN_DATE="${run_date}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
61 #end if
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
62
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
63 MIN_Q="${min_q}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
64 MAX_Q="${max_q}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
65 STRIP_UNPAIRED_MATE_NUMBER="${strip_unpairied_mate_number}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
66 ALLOW_AND_IGNORE_EMPTY_LINES="${allow_and_ignore_empty_lines}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
67
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
68 SORT_ORDER=coordinate
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
69 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
70 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
71 VERBOSITY=ERROR
20
2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents: 19
diff changeset
72 @TMPDIR_OPTION@
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
73 ]]></command>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
74 <inputs>
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
75 <conditional name="input_type">
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
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">
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
77 <option value="se">Single end (single dataset)</option>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
78 <option value="pe">Paired end (two datasets)</option>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
79 <option value="pc">Paired collection</option>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
80 </param>
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
81 <when value="se">
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
82 <param name="fastq" type="data" format="fastq" label="Input fastq file for single end data" help="FASTQ"/>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
83 </when>
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
84 <when value="pe">
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
85 <param name="fastq" type="data" format="fastq" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
86 <param name="fastq2" type="data" format="fastq" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
87 </when>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
88 <when value="pc">
9
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
89 <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"/>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
90 </when>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
91 </conditional>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
92
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
93 <param name="quality_format" type="select" label="Select quality encoding scheme" help="QUALITY_FORMAT">
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
94 <option value="Standard" selected="True">Sanger (+33)</option>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
95 <option value="Illumina">Illumina (+64)</option>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
96 <option value="Solexa">Solexa (+66)</option>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
97 </param>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
98
9
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
99 <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/>
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
100 <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
101 <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
102 <param name="platform_unit" type="text" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
103 <param name="platform" type="text" optional="True" label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
104 <param name="sequencing_center" type="text" optional="True" label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/>
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
105
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
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"/>
9
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
107 <param name="comment" type="text" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
108 <param name="description" type="text" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/>
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
109 <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
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"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
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"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
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"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
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"/>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
114
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
115 <expand macro="VS" />
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
116
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
117 </inputs>
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
118
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
119 <outputs>
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
120 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
121 </outputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
122
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
123 <tests>
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
124 <test>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
125 <param name="input_type_selector" value="pe" />
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
126 <param name="quality_format" value="Standard" />
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
127 <param name="read_group_name" value="A" />
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
128 <param name="sample_name" value="sample-a" />
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
129 <param name="library_name" value="A"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
130 <param name="platform_unit" value="A"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
131 <param name="platform" value="Illumina"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
132 <param name="sequencing_center" value="A"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
133 <param name="predicted_insert_size" value="300"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
134 <param name="comment" value="A"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
135 <param name="description" value="A"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
136 <param name="run_date" value="2014-10-10"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
137 <param name="min_q" value="0" />
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
138 <param name="max_q" value="93" />
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
139 <param name="strip_unpairied_mate_number" value="False" />
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
140 <param name="allow_and_ignore_empty_lines" value="False" />
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
141 <param name="validation_stringency" value="LENIENT"/>
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
142 <param name="fastq" value="picard_FastqToSam_read1.fq" ftype="fastq" />
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
143 <param name="fastq2" value="picard_FastqToSam_read2.fq" ftype="fastq" />
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
144 <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="bam" lines_diff="4"/>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
145 </test>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
146 </tests>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
147
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
148 <help>
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
149
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
150 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
151
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
152 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
153
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
154 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
155
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
156 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
157
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
158 @RG@
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
159
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
160 @description@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
161
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
162 FASTQ=File
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
163 F1=File Input fastq file for single end data, or first read in paired end
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
164 data. Required.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
165
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
166 FASTQ2=File
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
167 F2=File Input fastq file for the second read of paired end data (if used).
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
168
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
169 QUALITY_FORMAT=FastqQualityFormat
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
170 V=FastqQualityFormat A value describing how the quality values are encoded in the fastq. Either Solexa for
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
171 pre-pipeline 1.3 style scores (solexa scaling + 66), Illumina for pipeline 1.3 and above
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
172 (phred scaling + 64) or Standard for phred scaled scores with a character shift of 33.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
173 If this value is not specified, the quality format will be detected automatically.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
174 Default value: null. Possible values: {Solexa, Illumina, Standard}
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
175
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
176 READ_GROUP_NAME=String
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
177 RG=String Read group name Default value: A.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
178
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
179 SAMPLE_NAME=String
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
180 SM=String Sample name to insert into the read group header Required.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
181
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
182 LIBRARY_NAME=String
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
183 LB=String The library name to place into the LB attribute in the read group header.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
184
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
185 PLATFORM_UNIT=String
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
186 PU=String The platform unit (often run_barcode.lane) to insert into the read group header.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
187
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
188 PLATFORM=String
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
189 PL=String The platform type (e.g. illumina, solid) to insert into the read group header.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
190
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
191 SEQUENCING_CENTER=String
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
192 CN=String The sequencing center from which the data originated.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
193
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
194 PREDICTED_INSERT_SIZE=Integer
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
195 PI=Integer Predicted median insert size, to insert into the read group header.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
196
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
197 COMMENT=String
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
198 CO=String Comment to include in the merged output file's header.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
199
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
200 DESCRIPTION=String
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
201 DS=String Inserted into the read group header.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
202
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
203 RUN_DATE=Iso8601Date
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
204 DT=Iso8601Date Date the run was produced, to insert into the read group header.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
205
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
206 MIN_Q=Integer Minimum quality allowed in the input fastq. An exception will be thrown if a quality is
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
207 less than this value. Default value: 0.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
208
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
209 MAX_Q=Integer Maximum quality allowed in the input fastq. An exception will be thrown if a quality is
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
210 greater than this value. Default value: 93.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
211
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
212 STRIP_UNPAIRED_MATE_NUMBER=Boolean
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
213 If true and this is an unpaired fastq any occurance of '/1' will be removed from the end
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
214 of a read name. Default value: false. Possible values: {true, false}
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
215
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
216 ALLOW_AND_IGNORE_EMPTY_LINES=Boolean
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
217 Allow (and ignore) empty lines Default value: false. Possible values: {true, false}
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
218
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
219
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
220 @more_info@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
221
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
222 </help>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 13
diff changeset
223 <expand macro="citations" />
5
3d4f1fa26f0e Uploaded
devteam
parents: 3
diff changeset
224 </tool>