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comparison picard_CollectRnaSeqMetrics.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
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32:f9242e01365a 33:3f254c5ced1d
1 <tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
2 <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description> 2 <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</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 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="3.4.1">r-base</requirement> 8 <requirement type="package" version="447">ucsc-gff3togenepred</requirement>
9 <requirement type="package" version="357">ucsc-gff3togenepred</requirement> 9 <requirement type="package" version="447">ucsc-gtftogenepred</requirement>
10 <requirement type="package" version="357">ucsc-gtftogenepred</requirement>
11 </expand> 10 </expand>
12 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
13 ## Set up input files 12 ## Set up input files
14 @symlink_element_identifier@ 13 @symlink_element_identifier@
15 ## Reference sequences 14 ## Reference sequences
33 #end if 32 #end if
34 33
35 ## Start picard command 34 ## Start picard command
36 35
37 @java_options@ 36 @java_options@
38 picard 37 picard CollectRnaSeqMetrics
39 CollectRnaSeqMetrics 38 --REF_FLAT refFlat.tab
40 REF_FLAT=refFlat.tab
41 39
42 #if str( $ribosomal_intervals ) != "None": 40 #if str( $ribosomal_intervals ) != "None":
43 RIBOSOMAL_INTERVALS="${ribosomal_intervals}" 41 --RIBOSOMAL_INTERVALS '${ribosomal_intervals}'
44 #end if 42 #end if
45 43
46 STRAND_SPECIFICITY="${strand_specificity}" 44 --STRAND_SPECIFICITY '${strand_specificity}'
47 MINIMUM_LENGTH="${minimum_length}" 45 --MINIMUM_LENGTH '${minimum_length}'
48 CHART_OUTPUT="${pdfFile}" 46 --CHART_OUTPUT '${pdfFile}'
49 47
50 #for $sequence_to_ignore in $ignore_list: 48 #for $sequence_to_ignore in $ignore_list:
51 IGNORE_SEQUENCE="${sequence_to_ignore.sequence}" 49 --IGNORE_SEQUENCE '${sequence_to_ignore.sequence}'
52 #end for 50 #end for
53 51
54 RRNA_FRAGMENT_PERCENTAGE="${rrna_fragment_percentage}" 52 --RRNA_FRAGMENT_PERCENTAGE '${rrna_fragment_percentage}'
55 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" 53 --METRIC_ACCUMULATION_LEVEL '${metric_accumulation_level}'
56 INPUT='$escaped_element_identifier' 54 --INPUT '$escaped_element_identifier'
57 OUTPUT="${outFile}" 55 -OUTPUT '${outFile}'
58 REFERENCE_SEQUENCE="${reference_fasta_filename}" 56 --REFERENCE_SEQUENCE '${reference_fasta_filename}'
59 ASSUME_SORTED="${assume_sorted}" 57 --ASSUME_SORTED '${assume_sorted}'
60 VALIDATION_STRINGENCY=${validation_stringency} 58 --VALIDATION_STRINGENCY ${validation_stringency}
61 59
62 ]]></command> 60 ]]></command>
63 61 <inputs>
64 <inputs> 62 <param format="sam,bam" type="data" name="inputFile" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
65 <param format="sam,bam" type="data" name="inputFile" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> 63 <conditional name="reference_source">
66 <conditional name="reference_source"> 64 <param name="reference_source_selector" type="select" label="Load reference genome from">
67 <param name="reference_source_selector" type="select" label="Load reference genome from"> 65 <option value="cached">Local cache</option>
68 <option value="cached">Local cache</option> 66 <option value="history">History</option>
69 <option value="history">History</option>
70 </param>
71 <when value="cached">
72 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
73 <options from_data_table="all_fasta"></options>
74 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
75 </param> 67 </param>
76 </when> 68 <when value="cached">
77 <when value="history"> 69 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
78 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> 70 <options from_data_table="all_fasta"/>
79 </when> 71 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
80 </conditional> 72 </param>
81 73 </when>
82 <conditional name="gene_reference_source"> 74 <when value="history">
83 <param name="gene_reference_source_selector" type="select" label="Load gene annotation from"> 75 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference"/>
84 <option value="gtf">GTF/GFF3</option> 76 </when>
85 <option value="refflat">refFlat</option> 77 </conditional>
86 </param> 78 <conditional name="gene_reference_source">
87 <when value="gtf"> 79 <param name="gene_reference_source_selector" type="select" label="Load gene annotation from">
88 <param name="refFlat" 80 <option value="gtf">GTF/GFF3</option>
89 format="gtf,gff3" 81 <option value="refflat">refFlat</option>
90 type="data" 82 </param>
91 label="Gene annotation (GTF/GFF3)"/> 83 <when value="gtf">
92 </when> 84 <param name="refFlat" format="gtf,gff3" type="data" label="Gene annotation (GTF/GFF3)"/>
93 <when value="refflat"> 85 </when>
94 <param name="refFlat" 86 <when value="refflat">
95 format="tabular" 87 <param name="refFlat" format="tabular" type="data" label="Gene annotations in refFlat form" help="See &quot;Obtaining gene annotations in refFlat format&quot; below for help"/>
96 type="data" 88 </when>
97 label="Gene annotations in refFlat form" 89 </conditional>
98 help="See &quot;Obtaining gene annotations in refFlat format&quot; below for help"/> 90 <param name="ribosomal_intervals" format="picard_interval_list" type="data" optional="True" label="Location of rRNA sequences in genome, in interval_list format" help="RIBOSOMAL_INTERVALS; If not specified no bases will be identified as being ribosomal. The list of intervals can be geberated from BED or Interval datasets using Galaxy BedToIntervalList tool"/>
99 </when> 91 <param name="strand_specificity" type="select" label="What is the RNA-seq library strand specificity" help="STRAND_SPECIFICITY; For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand.">
100 </conditional> 92 <option value="NONE" selected="True">None</option>
101 93 <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option>
102 94 <option value="SECOND_READ_TRANSCRIPTION_STRAND">Second read transcription strand</option>
103 <param name="ribosomal_intervals" format="picard_interval_list" type="data" optional="True" label="Location of rRNA sequences in genome, in interval_list format" help="RIBOSOMAL_INTERVALS; If not specified no bases will be identified as being ribosomal. The list of intervals can be geberated from BED or Interval datasets using Galaxy BedToIntervalList tool"/> 95 </param>
104 <param name="strand_specificity" type="select" label="What is the RNA-seq library strand specificity" help="STRAND_SPECIFICITY; For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand."> 96 <param name="minimum_length" type="integer" value="500" label="When calculating coverage based values use only use transcripts of this length or greater" help="MINIMUM_LENGTH; default=500"/>
105 <option value="NONE" selected="True">None</option> 97 <repeat name="ignore_list" title="Sequences to ignore" min="0" help="You can provide multiple sequences by clicking the button below">
106 <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option> 98 <param name="sequence" type="text" label="Ignore reads matching this sequence"/>
107 <option value="SECOND_READ_TRANSCRIPTION_STRAND">Second read transcription strand</option> 99 </repeat>
108 </param> 100 <param name="rrna_fragment_percentage" type="float" value="0.8" label="This percentage of the length of a fragment must overlap one of the ribosomal intervals for a read or read pair to be considered rRNA." help="RRNA_FRAGMENT_PERCENTAGE; default=0.8"/>
109 <param name="minimum_length" type="integer" value="500" label="When calculating coverage based values use only use transcripts of this length or greater" help="MINIMUM_LENGTH; default=500"/> 101 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
110 <repeat name="ignore_list" title="Sequences to ignore" min="0" help="You can provide multiple sequences by clicking the button below"> 102 <option value="ALL_READS" selected="True">All reads</option>
111 <param name="sequence" type="text" label="Ignore reads matching this sequence"/> 103 <option value="SAMPLE">Sample</option>
112 </repeat> 104 <option value="LIBRARY">Library</option>
113 <param name="rrna_fragment_percentage" type="float" value="0.8" label="This percentage of the length of a fragment must overlap one of the ribosomal intervals for a read or read pair to be considered rRNA." help="RRNA_FRAGMENT_PERCENTAGE; default=0.8"/> 105 <option value="READ_GROUP">Read group</option>
114 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL"> 106 </param>
115 <option value="ALL_READS" selected="True">All reads</option> 107 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
116 <option value="SAMPLE">Sample</option> 108 <expand macro="VS"/>
117 <option value="LIBRARY">Library</option> 109 </inputs>
118 <option value="READ_GROUP">Read group</option> 110 <outputs>
119 </param> 111 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
120 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> 112 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
121 113 </outputs>
122 <expand macro="VS" /> 114 <tests>
123 115 <test>
124 </inputs> 116 <param name="reference_source_selector" value="history"/>
125 <outputs> 117 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
126 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> 118 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
127 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> 119 <param name="assume_sorted" value="true"/>
128 </outputs> 120 <param name="gene_reference_source_selector" value="refflat"/>
129 121 <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat"/>
130 <tests> 122 <param name="metric_accumulation_level" value="ALL_READS"/>
131 <test> 123 <param name="minimum_length" value="500"/>
132 <param name="reference_source_selector" value="history"/> 124 <param name="strand_specificity" value="NONE"/>
133 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> 125 <param name="rrna_fragment_percentage" value="0.8"/>
134 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> 126 <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
135 <param name="assume_sorted" value="true" /> 127 </test>
136 128 <test>
137 <param name="gene_reference_source_selector" value="refflat" /> 129 <param name="reference_source_selector" value="history"/>
138 <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat" /> 130 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
139 <param name="metric_accumulation_level" value="ALL_READS" /> 131 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
140 <param name="minimum_length" value="500" /> 132 <param name="assume_sorted" value="true"/>
141 <param name="strand_specificity" value="NONE" /> 133 <param name="gene_reference_source_selector" value="refflat"/>
142 <param name="rrna_fragment_percentage" value="0.8" /> 134 <param name="refFlat" value="picard_CollectRnaSeqMetrics.ucsc_output"/>
143 <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/> 135 <param name="metric_accumulation_level" value="ALL_READS"/>
144 </test> 136 <param name="minimum_length" value="500"/>
145 <test> 137 <param name="strand_specificity" value="NONE"/>
146 <param name="reference_source_selector" value="history"/> 138 <param name="rrna_fragment_percentage" value="0.8"/>
147 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> 139 <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
148 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> 140 </test>
149 <param name="assume_sorted" value="true" /> 141 <test>
150 142 <param name="reference_source_selector" value="history"/>
151 <param name="gene_reference_source_selector" value="refflat" /> 143 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
152 <param name="refFlat" value="picard_CollectRnaSeqMetrics.ucsc_output" /> 144 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
153 <param name="metric_accumulation_level" value="ALL_READS" /> 145 <param name="assume_sorted" value="true"/>
154 <param name="minimum_length" value="500" /> 146 <param name="gene_reference_source_selector" value="gtf"/>
155 <param name="strand_specificity" value="NONE" /> 147 <param name="refFlat" value="picard_CollectRnaSeqMetrics.gtf" ftype="gtf"/>
156 <param name="rrna_fragment_percentage" value="0.8" /> 148 <param name="metric_accumulation_level" value="ALL_READS"/>
157 <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/> 149 <param name="minimum_length" value="500"/>
158 </test> 150 <param name="strand_specificity" value="NONE"/>
159 151 <param name="rrna_fragment_percentage" value="0.8"/>
160 <test> 152 <output name="outFile" file="picard_CollectRnaSeqMetrics_test2.tab" ftype="tabular" lines_diff="4"/>
161 <param name="reference_source_selector" value="history"/> 153 </test>
162 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> 154 <test>
163 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> 155 <param name="reference_source_selector" value="history"/>
164 <param name="assume_sorted" value="true" /> 156 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
165 157 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
166 <param name="gene_reference_source_selector" value="gtf" /> 158 <param name="assume_sorted" value="true"/>
167 <param name="refFlat" value="picard_CollectRnaSeqMetrics.gtf" ftype="gtf" /> 159 <param name="gene_reference_source_selector" value="gtf"/>
168 <param name="metric_accumulation_level" value="ALL_READS" /> 160 <param name="refFlat" value="picard_CollectRnaSeqMetrics.gff3" ftype="gff3"/>
169 <param name="minimum_length" value="500" /> 161 <param name="metric_accumulation_level" value="ALL_READS"/>
170 <param name="strand_specificity" value="NONE" /> 162 <param name="minimum_length" value="500"/>
171 <param name="rrna_fragment_percentage" value="0.8" /> 163 <param name="strand_specificity" value="NONE"/>
172 <output name="outFile" file="picard_CollectRnaSeqMetrics_test2.tab" ftype="tabular" lines_diff="4"/> 164 <param name="rrna_fragment_percentage" value="0.8"/>
173 </test> 165 <output name="outFile" file="picard_CollectRnaSeqMetrics_test3.tab" ftype="tabular" lines_diff="4"/>
174 166 </test>
175 <test> 167 </tests>
176 <param name="reference_source_selector" value="history"/> 168 <help>
177 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
178 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
179 <param name="assume_sorted" value="true" />
180
181 <param name="gene_reference_source_selector" value="gtf" />
182 <param name="refFlat" value="picard_CollectRnaSeqMetrics.gff3" ftype="gff3" />
183 <param name="metric_accumulation_level" value="ALL_READS" />
184 <param name="minimum_length" value="500" />
185 <param name="strand_specificity" value="NONE" />
186 <param name="rrna_fragment_percentage" value="0.8" />
187 <output name="outFile" file="picard_CollectRnaSeqMetrics_test3.tab" ftype="tabular" lines_diff="4"/>
188 </test>
189 </tests>
190 <help>
191 169
192 .. class:: infomark 170 .. class:: infomark
193 171
194 **Purpose** 172 **Purpose**
195 173
263 value: true. Possible values: {true, false} 241 value: true. Possible values: {true, false}
264 242
265 @more_info@ 243 @more_info@
266 244
267 </help> 245 </help>
268 <expand macro="citations" /> 246 <expand macro="citations"/>
269 </tool> 247 </tool>