Mercurial > repos > nilesh > rseqc
comparison junction_annotation.xml @ 51:09846d5169fa draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author | iuc |
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date | Tue, 14 Mar 2017 10:23:21 -0400 |
parents | 6b33e31bda10 |
children | 34e4c586e3c0 |
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50:f242ee103277 | 51:09846d5169fa |
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1 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="2.4galaxy1"> | 1 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="@WRAPPER_VERSION@"> |
2 <description>compares detected splice junctions to reference gene model</description> | 2 <description>compares detected splice junctions to reference gene model</description> |
3 | 3 |
4 <macros> | 4 <macros> |
5 <import>rseqc_macros.xml</import> | 5 <import>rseqc_macros.xml</import> |
6 </macros> | 6 </macros> |
7 | 7 |
8 <requirements> | 8 <expand macro="requirements" /> |
9 <expand macro="requirement_package_r" /> | |
10 <expand macro="requirement_package_numpy" /> | |
11 <expand macro="requirement_package_rseqc" /> | |
12 </requirements> | |
13 | 9 |
14 <expand macro="stdio" /> | 10 <expand macro="stdio" /> |
15 | 11 |
16 <version_command><![CDATA[junction_annotation.py --version]]></version_command> | 12 <version_command><![CDATA[junction_annotation.py --version]]></version_command> |
17 | 13 |
18 <command><![CDATA[ | 14 <command><![CDATA[ |
19 junction_annotation.py | 15 junction_annotation.py |
20 --input-file $input | 16 --input-file '${input}' |
21 --refgene $refgene | 17 --refgene '${refgene}' |
22 --out-prefix output | 18 --out-prefix output |
23 --min-intron $min_intron | 19 --min-intron ${min_intron} |
24 --mapq $mapq | 20 --mapq ${mapq} |
25 ]]> | 21 ]]> |
26 </command> | 22 </command> |
27 | 23 |
28 <inputs> | 24 <inputs> |
29 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/> | 25 <expand macro="bam_sam_param" /> |
30 <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/> | 26 <expand macro="refgene_param" /> |
31 <param name="min_intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" help="(--min-intron)" /> | 27 <expand macro="min_intron_param" /> |
32 <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" /> | 28 <expand macro="mapq_param" /> |
29 <expand macro="rscript_output_param" /> | |
33 </inputs> | 30 </inputs> |
34 | 31 |
35 <outputs> | 32 <outputs> |
36 <data format="xls" name="outputxls" from_work_dir="output.junction.xls" label="${tool.name} on ${on_string} (XLS)"/> | 33 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events pdf)"/> |
37 <data format="txt" name="outputr" from_work_dir="output.junction_plot.r" label="${tool.name} on ${on_string} (R Script)" /> | 34 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction pdf)" /> |
38 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events PDF)"/> | 35 <expand macro="xls_output_data" filename="output.junction.xls" /> |
39 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction PDF)" /> | 36 <expand macro="rscript_output_data" filename="output.junction_plot.r" /> |
40 </outputs> | 37 </outputs> |
41 | 38 |
42 <tests> | 39 <tests> |
43 <test> | 40 <test> |
44 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> | 41 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> |
45 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/> | 42 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" /> |
46 <output name="outputxls" file="output.junction.xls"/> | 43 <param name="rscript_output" value="true" /> |
47 <output name="outputr" file="output.junction_plot.r"/> | 44 <output name="outputxls" file="output.junction.xls" /> |
48 <output name="outputpdf" file="output.splice_events.pdf"/> | 45 <output name="outputr" file="output.junction_plot.r" /> |
49 <output name="outputjpdf" file="output.splice_junction.pdf"/> | 46 <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" /> |
47 <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size" /> | |
50 </test> | 48 </test> |
51 </tests> | 49 </tests> |
52 | 50 |
53 <help><![CDATA[ | 51 <help><![CDATA[ |
54 junction_annotation.py | 52 junction_annotation.py |
92 - 'annotated', 'complete_novel' or 'partial_novel'. | 90 - 'annotated', 'complete_novel' or 'partial_novel'. |
93 2. output.anno.junction_plot.r: R script to generate pie chart | 91 2. output.anno.junction_plot.r: R script to generate pie chart |
94 3. output.splice_junction.pdf: plot of splice junctions | 92 3. output.splice_junction.pdf: plot of splice junctions |
95 4. output.splice_events.pdf: plot of splice events | 93 4. output.splice_events.pdf: plot of splice events |
96 | 94 |
97 .. image:: http://rseqc.sourceforge.net/_images/junction.png | 95 .. image:: $PATH_TO_IMAGES/junction.png |
98 :height: 400 px | 96 :height: 400 px |
99 :width: 850 px | 97 :width: 850 px |
100 :scale: 80 % | 98 :scale: 80 % |
101 | 99 |
102 ----- | 100 @ABOUT@ |
103 | 101 |
104 About RSeQC | |
105 +++++++++++ | |
106 | |
107 The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation. | |
108 | |
109 The RSeQC package is licensed under the GNU GPL v3 license. | |
110 | |
111 .. image:: http://rseqc.sourceforge.net/_static/logo.png | |
112 | |
113 .. _RSeQC: http://rseqc.sourceforge.net/ | |
114 ]]> | 102 ]]> |
115 </help> | 103 </help> |
116 | 104 |
117 <expand macro="citations" /> | 105 <expand macro="citations" /> |
118 | 106 |