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comparison picard_FastqToSam.xml @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
comparison
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32:f9242e01365a 33:3f254c5ced1d
1 <tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="20.01"> 1 <tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
2 <description>convert Fastq data into unaligned BAM</description> 2 <description>convert Fastq data into unaligned BAM</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <token name="@WRAPPER_VERSION@">2</token> 5 <token name="@WRAPPER_VERSION@">0</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">picard_fastqtosam</xref> 8 <xref type="bio.tools">picard_fastqtosam</xref>
9 </xrefs> 9 </xrefs>
10 <expand macro="requirements" /> 10 <expand macro="requirements"/>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 @java_options@ 12 @java_options@
13 #if str( $input_type.input_type_selector ) == "se": 13 #if str( $input_type.input_type_selector ) == "se":
14 #set fwd = $input_type.fastq 14 #set fwd = $input_type.fastq
15 #set rev = None 15 #set rev = None
22 #end if 22 #end if
23 23
24 #if $fwd.ext.endswith(".gz") 24 #if $fwd.ext.endswith(".gz")
25 gunzip -c '$fwd' > fwd.fastq && 25 gunzip -c '$fwd' > fwd.fastq &&
26 #else 26 #else
27 ln -s '$fwd' fwd.fastq && 27 ln -sf '$fwd' fwd.fastq &&
28 #end if 28 #end if
29 #if rev 29 #if rev
30 #if rev.ext.endswith(".gz") 30 #if rev.ext.endswith(".gz")
31 gunzip -c '$rev' > rev.fastq && 31 gunzip -c '$rev' > rev.fastq &&
32 #else 32 #else
33 ln -s '$rev' rev.fastq && 33 ln -sf '$rev' rev.fastq &&
34 #end if 34 #end if
35 #end if 35 #end if
36 36
37 picard 37 picard FastqToSam
38 FastqToSam 38
39 39 --FASTQ fwd.fastq
40 FASTQ=fwd.fastq
41 #if rev 40 #if rev
42 FASTQ2=rev.fastq 41 --FASTQ2 rev.fastq
43 #end if 42 #end if
44 43
45 #if $fwd.ext.startswith("fastqillumina") 44 #if $fwd.ext.startswith("fastqillumina")
46 QUALITY_FORMAT="Illumina" 45 --QUALITY_FORMAT "Illumina"
47 #else if $fwd.ext.startswith("fastqsolexa") 46 #else if $fwd.ext.startswith("fastqsolexa")
48 QUALITY_FORMAT="Solexa" 47 --QUALITY_FORMAT "Solexa"
49 #else 48 #else
50 QUALITY_FORMAT="Standard" 49 --QUALITY_FORMAT "Standard"
51 #end if 50 #end if
52 OUTPUT="${outFile}" 51 --OUTPUT '${outFile}'
53 READ_GROUP_NAME="${read_group_name}" 52 --READ_GROUP_NAME '${read_group_name}'
54 SAMPLE_NAME="${sample_name}" 53 --SAMPLE_NAME '${sample_name}'
55 54
56 #if str( $library_name ): 55 #if str( $library_name ):
57 LIBRARY_NAME="${library_name}" 56 --LIBRARY_NAME '${library_name}'
58 #end if 57 #end if
59 58
60 #if str( $platform_unit ): 59 #if str( $platform_unit ):
61 PLATFORM_UNIT="${platform_unit}" 60 --PLATFORM_UNIT '${platform_unit}'
62 #end if 61 #end if
63 62
64 #if str( $platform ): 63 #if str( $platform ):
65 PLATFORM="${platform}" 64 --PLATFORM '${platform}'
66 #end if 65 #end if
67 66
68 #if str( $sequencing_center ): 67 #if str( $sequencing_center ):
69 SEQUENCING_CENTER="${sequencing_center}" 68 --SEQUENCING_CENTER '${sequencing_center}'
70 #end if 69 #end if
71 70
72 #if str( $predicted_insert_size ): 71 #if str( $predicted_insert_size ):
73 PREDICTED_INSERT_SIZE="${predicted_insert_size}" 72 --PREDICTED_INSERT_SIZE '${predicted_insert_size}'
74 #end if 73 #end if
75 74
76 #if str( $comment ): 75 #if str( $comment ):
77 COMMENT="${comment}" 76 --COMMENT '${comment}'
78 #end if 77 #end if
79 78
80 #if str( $description ): 79 #if str( $description ):
81 DESCRIPTION="${description}" 80 --DESCRIPTION '${description}'
82 #end if 81 #end if
83 82
84 #if str( $run_date ): 83 #if str( $run_date ):
85 RUN_DATE="${run_date}" 84 --RUN_DATE '${run_date}'
86 #end if 85 #end if
87 86
88 MIN_Q="${min_q}" 87 --MIN_Q '${min_q}'
89 MAX_Q="${max_q}" 88 --MAX_Q '${max_q}'
90 STRIP_UNPAIRED_MATE_NUMBER="${strip_unpairied_mate_number}" 89 --STRIP_UNPAIRED_MATE_NUMBER '${strip_unpairied_mate_number}'
91 ALLOW_AND_IGNORE_EMPTY_LINES="${allow_and_ignore_empty_lines}" 90 --ALLOW_AND_IGNORE_EMPTY_LINES '${allow_and_ignore_empty_lines}'
92 91
93 SORT_ORDER=coordinate 92 --SORT_ORDER coordinate
94 VALIDATION_STRINGENCY="${validation_stringency}" 93 --VALIDATION_STRINGENCY '${validation_stringency}'
95 QUIET=true 94 --QUIET true
96 VERBOSITY=ERROR 95 --VERBOSITY ERROR
96
97 ]]></command> 97 ]]></command>
98 <inputs> 98 <inputs>
99 <conditional name="input_type"> 99 <conditional name="input_type">
100 <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"> 100 <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">
101 <option value="se">Single end (single dataset)</option> 101 <option value="se">Single end (single dataset)</option>
102 <option value="pe">Paired end (two datasets)</option> 102 <option value="pe">Paired end (two datasets)</option>
103 <option value="pc">Paired collection</option> 103 <option value="pc">Paired collection</option>
104 </param> 104 </param>
105 <when value="se"> 105 <when value="se">
106 <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for single end data" help="FASTQ"/> 106 <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for single end data" help="FASTQ"/>
107 </when> 107 </when>
108 <when value="pe"> 108 <when value="pe">
109 <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for the first read in paired end data" help="FASTQ"/> 109 <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
110 <param name="fastq2" type="data" format="fastq,fastq.gz" label="Input fastq file for the second read of paired end data" help="FASTQ2"/> 110 <param name="fastq2" type="data" format="fastq,fastq.gz" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
111 </when> 111 </when>
112 <when value="pc"> 112 <when value="pc">
113 <param name="fastq" type="data_collection" collection_type="paired" format="fastq,fastq.gz" 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"/> 113 <param name="fastq" type="data_collection" collection_type="paired" format="fastq,fastq.gz" 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"/>
114 </when> 114 </when>
115 </conditional> 115 </conditional>
116 116 <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/>
117 <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/> 117 <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
118 <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/> 118 <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
119 <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/> 119 <param name="platform_unit" type="text" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
120 <param name="platform_unit" type="text" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/> 120 <param name="platform" type="text" optional="True" label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
121 <param name="platform" type="text" optional="True" label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/> 121 <param name="sequencing_center" type="text" optional="True" label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/>
122 <param name="sequencing_center" type="text" optional="True" label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/> 122 <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"/>
123 123 <param name="comment" type="text" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
124 <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"/> 124 <param name="description" type="text" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/>
125 <param name="comment" type="text" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/> 125 <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
126 <param name="description" type="text" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/> 126 <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"/>
127 <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/> 127 <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"/>
128 <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"/> 128 <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"/>
129 <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"/> 129 <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"/>
130 <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"/> 130 <expand macro="VS"/>
131 <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"/> 131 </inputs>
132 132 <outputs>
133 <expand macro="VS" /> 133 <data format="unsorted.bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/>
134 134 </outputs>
135 </inputs> 135 <tests>
136 136 <test>
137 <outputs> 137 <param name="input_type_selector" value="pe"/>
138 <data format="unsorted.bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/> 138 <param name="read_group_name" value="A"/>
139 </outputs> 139 <param name="sample_name" value="sample-a"/>
140 140 <param name="library_name" value="A"/>
141 <tests> 141 <param name="platform_unit" value="A"/>
142 <test> 142 <param name="platform" value="Illumina"/>
143 <param name="input_type_selector" value="pe" /> 143 <param name="sequencing_center" value="A"/>
144 <param name="read_group_name" value="A" /> 144 <param name="predicted_insert_size" value="300"/>
145 <param name="sample_name" value="sample-a" /> 145 <param name="comment" value="A"/>
146 <param name="library_name" value="A"/> 146 <param name="description" value="A"/>
147 <param name="platform_unit" value="A"/> 147 <param name="run_date" value="2014-10-10"/>
148 <param name="platform" value="Illumina"/> 148 <param name="min_q" value="0"/>
149 <param name="sequencing_center" value="A"/> 149 <param name="max_q" value="93"/>
150 <param name="predicted_insert_size" value="300"/> 150 <param name="strip_unpairied_mate_number" value="False"/>
151 <param name="comment" value="A"/> 151 <param name="allow_and_ignore_empty_lines" value="False"/>
152 <param name="description" value="A"/> 152 <param name="validation_stringency" value="LENIENT"/>
153 <param name="run_date" value="2014-10-10"/> 153 <param name="fastq" value="picard_FastqToSam_read1.fq.gz" ftype="fastq.gz"/>
154 <param name="min_q" value="0" /> 154 <param name="fastq2" value="picard_FastqToSam_read2.fq.gz" ftype="fastq.gz"/>
155 <param name="max_q" value="93" /> 155 <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="unsorted.bam" lines_diff="4"/>
156 <param name="strip_unpairied_mate_number" value="False" /> 156 </test>
157 <param name="allow_and_ignore_empty_lines" value="False" /> 157 </tests>
158 <param name="validation_stringency" value="LENIENT"/> 158 <help>
159 <param name="fastq" value="picard_FastqToSam_read1.fq.gz" ftype="fastq.gz" />
160 <param name="fastq2" value="picard_FastqToSam_read2.fq.gz" ftype="fastq.gz" />
161 <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="unsorted.bam" lines_diff="4"/>
162 </test>
163 </tests>
164
165 <help>
166 159
167 .. class:: infomark 160 .. class:: infomark
168 161
169 **Purpose** 162 **Purpose**
170 163
235 228
236 229
237 @more_info@ 230 @more_info@
238 231
239 </help> 232 </help>
240 <expand macro="citations" /> 233 <expand macro="citations"/>
241 </tool> 234 </tool>