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comparison read_GC.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
equal deleted inserted replaced
50:f242ee103277 51:09846d5169fa
1 <tool id="rseqc_read_GC" name="Read GC" version="2.4galaxy1"> 1 <tool id="rseqc_read_GC" name="Read GC" version="@WRAPPER_VERSION@">
2 <description>determines GC% and read count</description> 2 <description>determines GC% and read count</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_GC.py --version]]></version_command> 12 <version_command><![CDATA[read_GC.py --version]]></version_command>
17 13
18 <command><![CDATA[ 14 <command><![CDATA[
19 read_GC.py 15 read_GC.py
20 --input-file $input 16 --input-file '${input}'
21 --out-prefix output 17 --out-prefix output
22 --mapq $mapq 18 --mapq ${mapq}
23 ]]> 19 ]]>
24 </command> 20 </command>
25 21
26 <inputs> 22 <inputs>
27 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/> 23 <expand macro="bam_sam_param" />
28 <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" /> 24 <expand macro="mapq_param" />
25 <expand macro="rscript_output_param" />
29 </inputs> 26 </inputs>
30 27
31 <outputs> 28 <outputs>
32 <data format="xls" name="outputxls" from_work_dir="output.GC.xls" label="${tool.name} on ${on_string} (XLS)"/> 29 <expand macro="pdf_output_data" filename="output.GC_plot.pdf" />
33 <data format="txt" name="outputr" from_work_dir="output.GC_plot.r" label="${tool.name} on ${on_string} (R Script)" /> 30 <expand macro="xls_output_data" filename="output.GC.xls" />
34 <data format="pdf" name="outputpdf" from_work_dir="output.GC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" /> 31 <expand macro="rscript_output_data" filename="output.GC_plot.r" />
35 </outputs> 32 </outputs>
36 33
37 <tests> 34 <tests>
38 <test> 35 <test>
39 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 36 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
40 <output name="outputxls" file="output.GC.xls"/> 37 <param name="rscript_output" value="true" />
41 <output name="outputr" file="output.GC_plot.r"/> 38 <output name="outputxls" file="output.GC.xls" />
39 <output name="outputr" file="output.GC_plot.r" />
40 <output name="outputpdf" file="output.GC_plot.pdf" compare="sim_size" />
42 </test> 41 </test>
43 </tests> 42 </tests>
44 43
45 <help><![CDATA[ 44 <help><![CDATA[
46 read_GC.py 45 read_GC.py
58 57
59 1. output.GC.xls: Two column, plain text file, first column is GC%, second column is read count 58 1. output.GC.xls: Two column, plain text file, first column is GC%, second column is read count
60 2. output.GC_plot.r: R script to generate pdf file. 59 2. output.GC_plot.r: R script to generate pdf file.
61 3. output.GC_plot.pdf: graphical output generated from R script. 60 3. output.GC_plot.pdf: graphical output generated from R script.
62 61
63 .. image:: http://rseqc.sourceforge.net/_images/read_gc.png 62 .. image:: $PATH_TO_IMAGES/read_gc.png
64 :height: 600 px 63 :height: 600 px
65 :width: 600 px 64 :width: 600 px
66 :scale: 80 % 65 :scale: 80 %
67 66
68 ----- 67 @ABOUT@
69 68
70 About RSeQC
71 +++++++++++
72
73 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.
74
75 The RSeQC package is licensed under the GNU GPL v3 license.
76
77 .. image:: http://rseqc.sourceforge.net/_static/logo.png
78
79 .. _RSeQC: http://rseqc.sourceforge.net/
80 ]]> 69 ]]>
81 </help> 70 </help>
82 71
83 <expand macro="citations" /> 72 <expand macro="citations" />
84 73