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comparison picard_CollectRnaSeqMetrics.xml @ 27:a1f0b3f4b781 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 11b94d7cd69b919f16feb10bd4b830a963334ab8"
author iuc
date Wed, 19 Feb 2020 14:27:00 -0500
parents f6ced08779c4
children f9242e01365a
comparison
equal deleted inserted replaced
26:9ffcddf6f9c0 27:a1f0b3f4b781
1 <tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 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@">1</token> 5 <token name="@WRAPPER_VERSION@">2</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="3.4.1">r-base</requirement>
9 <requirement type="package" version="357">ucsc-gff3togenepred</requirement> 9 <requirement type="package" version="357">ucsc-gff3togenepred</requirement>
10 <requirement type="package" version="357">ucsc-gtftogenepred</requirement> 10 <requirement type="package" version="357">ucsc-gtftogenepred</requirement>
20 20
21 ## refFlat data 21 ## refFlat data
22 ## 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
23 23
24 #if str($gene_reference_source.gene_reference_source_selector) == "gtf" 24 #if str($gene_reference_source.gene_reference_source_selector) == "gtf"
25 #if $gene_reference_source.refFlat.ext != 'gff3' 25 #if $gene_reference_source.refFlat.ext == 'gff3'
26 gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw &&
27 #else
26 gtfToGenePred -genePredExt '${gene_reference_source.refFlat}' refFlat.tab.raw && 28 gtfToGenePred -genePredExt '${gene_reference_source.refFlat}' refFlat.tab.raw &&
27 #else
28 gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw &&
29 #end if 29 #end if
30
31 grep -v '^#' refFlat.tab.raw | awk '{print $12"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab && 30 grep -v '^#' refFlat.tab.raw | awk '{print $12"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab &&
32 #else 31 #else
33 grep -v '^#' ${refFlat} | awk '{print $11"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab && 32 grep -v '^#' ${refFlat} | awk '{if ($3 == "+" || $3 == "-") print $11"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10; else print}' > refFlat.tab &&
34 #end if 33 #end if
35
36 34
37 ## Start picard command 35 ## Start picard command
38 36
39 @java_options@ 37 @java_options@
40 picard 38 picard
137 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> 135 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
138 <param name="assume_sorted" value="true" /> 136 <param name="assume_sorted" value="true" />
139 137
140 <param name="gene_reference_source_selector" value="refflat" /> 138 <param name="gene_reference_source_selector" value="refflat" />
141 <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat" /> 139 <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat" />
140 <param name="metric_accumulation_level" value="ALL_READS" />
141 <param name="minimum_length" value="500" />
142 <param name="strand_specificity" value="NONE" />
143 <param name="rrna_fragment_percentage" value="0.8" />
144 <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
145 </test>
146 <test>
147 <param name="reference_source_selector" value="history"/>
148 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
149 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
150 <param name="assume_sorted" value="true" />
151
152 <param name="gene_reference_source_selector" value="refflat" />
153 <param name="refFlat" value="picard_CollectRnaSeqMetrics.ucsc_output" />
142 <param name="metric_accumulation_level" value="ALL_READS" /> 154 <param name="metric_accumulation_level" value="ALL_READS" />
143 <param name="minimum_length" value="500" /> 155 <param name="minimum_length" value="500" />
144 <param name="strand_specificity" value="NONE" /> 156 <param name="strand_specificity" value="NONE" />
145 <param name="rrna_fragment_percentage" value="0.8" /> 157 <param name="rrna_fragment_percentage" value="0.8" />
146 <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/> 158 <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>