Mercurial > repos > devteam > picard
comparison picard_CollectRnaSeqMetrics.xml @ 22:81de93de916f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 11b94d7cd69b919f16feb10bd4b830a963334ab8"
author | iuc |
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date | Wed, 19 Feb 2020 19:26:15 +0000 |
parents | 2474cd44d10a |
children | c943f4a04af0 |
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21:1181366ba593 | 22:81de93de916f |
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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"/> |