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comparison read_duplication.xml @ 51:09846d5169fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author iuc
date Tue, 14 Mar 2017 10:23:21 -0400
parents 6b33e31bda10
children dbedfc5f5a3c
comparison
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50:f242ee103277 51:09846d5169fa
1 <tool id="rseqc_read_duplication" name="Read Duplication" version="2.4galaxy1"> 1 <tool id="rseqc_read_duplication" name="Read Duplication" version="@WRAPPER_VERSION@">
2 <description>determines reads duplication rate with sequence-based and mapping-based strategies</description> 2 <description>determines reads duplication rate with sequence-based and mapping-based strategies</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[read_duplication.py --version]]></version_command> 12 <version_command><![CDATA[read_duplication.py --version]]></version_command>
17 13
18 <command><![CDATA[ 14 <command><![CDATA[
19 read_duplication.py -i $input -o output -u $upLimit 15 read_duplication.py -i '${input}' -o output -u ${upLimit} -q ${mapq}
20 ]]> 16 ]]>
21 </command> 17 </command>
22 18
23 <inputs> 19 <inputs>
24 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/> 20 <expand macro="bam_sam_param" />
25 <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" help="(--up-limit)"/> 21 <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" help="(--up-limit)"/>
22 <expand macro="mapq_param" />
23 <expand macro="rscript_output_param" />
26 </inputs> 24 </inputs>
27 25
28 <outputs> 26 <outputs>
29 <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position XLS)"/> 27 <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf" />
30 <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence XLS)"/> 28 <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position xls)"/>
31 <data format="txt" name="outputr" from_work_dir="output.DupRate_plot.r" label="${tool.name} on ${on_string} (R Script)" /> 29 <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence xls)"/>
32 <data format="pdf" name="outputpdf" from_work_dir="output.DupRate_plot.pdf" label="${tool.name} on ${on_string} (PDF)" /> 30 <expand macro="rscript_output_data" filename="output.DupRate_plot.r" />
33 </outputs> 31 </outputs>
34 32
35 <tests> 33 <tests>
36 <test> 34 <test>
37 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 35 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
38 <output name="outputxls" file="output.pos.DupRate.xls"/> 36 <param name="rscript_output" value="true" />
39 <output name="outputseqxls" file="output.seq.DupRate.xls"/> 37 <output name="outputxls" file="output.pos.DupRate.xls" />
40 <output name="outputr" file="output.DupRate_plot.r"/> 38 <output name="outputseqxls" file="output.seq.DupRate.xls" />
39 <output name="outputr" file="output.DupRate_plot.r" />
40 <output name="outputpdf" file="output.DupRate_plot.pdf" compare="sim_size" />
41 </test> 41 </test>
42 </tests> 42 </tests>
43 43
44 <help><![CDATA[ 44 <help><![CDATA[
45 read_duplication.py 45 read_duplication.py
65 1. output.dup.pos.DupRate.xls: Read duplication rate determined from mapping position of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads. 65 1. output.dup.pos.DupRate.xls: Read duplication rate determined from mapping position of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads.
66 2. output.dup.seq.DupRate.xls: Read duplication rate determined from sequence of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads. 66 2. output.dup.seq.DupRate.xls: Read duplication rate determined from sequence of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads.
67 3. output.DupRate_plot.r: R script to generate pdf file 67 3. output.DupRate_plot.r: R script to generate pdf file
68 4. output.DupRate_plot.pdf: graphical output generated from R script 68 4. output.DupRate_plot.pdf: graphical output generated from R script
69 69
70 .. image:: http://rseqc.sourceforge.net/_images/duplicate.png 70 .. image:: $PATH_TO_IMAGES/duplicate.png
71 :height: 600 px 71 :height: 600 px
72 :width: 600 px 72 :width: 600 px
73 :scale: 80 % 73 :scale: 80 %
74 74
75 ----- 75 @ABOUT@
76 76
77 About RSeQC
78 +++++++++++
79
80 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.
81
82 The RSeQC package is licensed under the GNU GPL v3 license.
83
84 .. image:: http://rseqc.sourceforge.net/_static/logo.png
85
86 .. _RSeQC: http://rseqc.sourceforge.net/
87 ]]> 77 ]]>
88 </help> 78 </help>
89 79
90 <expand macro="citations" /> 80 <expand macro="citations" />
91 81