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comparison picard_CollectRnaSeqMetrics.xml @ 19:5053a18d9bc8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
author iuc
date Mon, 16 Apr 2018 21:27:29 -0400
parents fc288950c3b7
children 2a17c789e0a5
comparison
equal deleted inserted replaced
18:7615ac66c6e5 19:5053a18d9bc8
1 <tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.1"> 1 <tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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@">0</token>
5 </macros> 6 </macros>
6 <expand macro="requirements"> 7 <expand macro="requirements">
7 <requirement type="package" version="3.3.1">r</requirement> 8 <requirement type="package" version="3.4.1">r-base</requirement>
8 <requirement type="package" version="324">ucsc-gff3togenepred</requirement> 9 <requirement type="package" version="357">ucsc-gff3togenepred</requirement>
9 <requirement type="package" version="324">ucsc-gtftogenepred</requirement> 10 <requirement type="package" version="357">ucsc-gtftogenepred</requirement>
10 </expand> 11 </expand>
11 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
12 ## Set up input files 13 ## Set up input files
13 @symlink_element_identifier@ 14 @symlink_element_identifier@
14 ## Reference sequences 15 ## Reference sequences
15 16
16 #set $reference_fasta_filename = "localref.fa" 17 #set $reference_fasta_filename = "localref.fa"
17 18
18 #if str( $reference_source.reference_source_selector ) == "history": 19 @handle_reference_source@
19 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
20 #else:
21 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
22 #end if
23 20
24 ## refFlat data 21 ## refFlat data
25 ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format 22 ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format
26 23
27 #if str($gene_reference_source.gene_reference_source_selector) == "gtf" 24 #if str($gene_reference_source.gene_reference_source_selector) == "gtf"
60 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" 57 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
61 INPUT='$escaped_element_identifier' 58 INPUT='$escaped_element_identifier'
62 OUTPUT="${outFile}" 59 OUTPUT="${outFile}"
63 REFERENCE_SEQUENCE="${reference_fasta_filename}" 60 REFERENCE_SEQUENCE="${reference_fasta_filename}"
64 ASSUME_SORTED="${assume_sorted}" 61 ASSUME_SORTED="${assume_sorted}"
65 62
66 VALIDATION_STRINGENCY=${validation_stringency} 63 VALIDATION_STRINGENCY=${validation_stringency}
67 64
68 ]]></command> 65 ]]></command>
69 66
70 <inputs> 67 <inputs>
137 <test> 134 <test>
138 <param name="reference_source_selector" value="history"/> 135 <param name="reference_source_selector" value="history"/>
139 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> 136 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
140 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> 137 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
141 <param name="assume_sorted" value="true" /> 138 <param name="assume_sorted" value="true" />
142 139
143 <param name="gene_reference_source_selector" value="refflat" /> 140 <param name="gene_reference_source_selector" value="refflat" />
144 <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat" /> 141 <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat" />
145 <param name="metric_accumulation_level" value="ALL_READS" /> 142 <param name="metric_accumulation_level" value="ALL_READS" />
146 <param name="minimum_length" value="500" /> 143 <param name="minimum_length" value="500" />
147 <param name="strand_specificity" value="NONE" /> 144 <param name="strand_specificity" value="NONE" />
152 <test> 149 <test>
153 <param name="reference_source_selector" value="history"/> 150 <param name="reference_source_selector" value="history"/>
154 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> 151 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
155 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> 152 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
156 <param name="assume_sorted" value="true" /> 153 <param name="assume_sorted" value="true" />
157 154
158 <param name="gene_reference_source_selector" value="gtf" /> 155 <param name="gene_reference_source_selector" value="gtf" />
159 <param name="refFlat" value="picard_CollectRnaSeqMetrics.gtf" ftype="gtf" /> 156 <param name="refFlat" value="picard_CollectRnaSeqMetrics.gtf" ftype="gtf" />
160 <param name="metric_accumulation_level" value="ALL_READS" /> 157 <param name="metric_accumulation_level" value="ALL_READS" />
161 <param name="minimum_length" value="500" /> 158 <param name="minimum_length" value="500" />
162 <param name="strand_specificity" value="NONE" /> 159 <param name="strand_specificity" value="NONE" />
167 <test> 164 <test>
168 <param name="reference_source_selector" value="history"/> 165 <param name="reference_source_selector" value="history"/>
169 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> 166 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
170 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> 167 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
171 <param name="assume_sorted" value="true" /> 168 <param name="assume_sorted" value="true" />
172 169
173 <param name="gene_reference_source_selector" value="gtf" /> 170 <param name="gene_reference_source_selector" value="gtf" />
174 <param name="refFlat" value="picard_CollectRnaSeqMetrics.gff3" ftype="gff3" /> 171 <param name="refFlat" value="picard_CollectRnaSeqMetrics.gff3" ftype="gff3" />
175 <param name="metric_accumulation_level" value="ALL_READS" /> 172 <param name="metric_accumulation_level" value="ALL_READS" />
176 <param name="minimum_length" value="500" /> 173 <param name="minimum_length" value="500" />
177 <param name="strand_specificity" value="NONE" /> 174 <param name="strand_specificity" value="NONE" />
255 value: true. Possible values: {true, false} 252 value: true. Possible values: {true, false}
256 253
257 @more_info@ 254 @more_info@
258 255
259 </help> 256 </help>
257 <expand macro="citations" />
260 </tool> 258 </tool>