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comparison read_quality.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 f242ee103277
children 34e4c586e3c0
comparison
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50:f242ee103277 51:09846d5169fa
1 <tool id="rseqc_read_quality" name="Read Quality" version="2.4galaxy1"> 1 <tool id="rseqc_read_quality" name="Read Quality" version="@WRAPPER_VERSION@">
2 <description>determines Phred quality score</description> 2 <description>determines Phred quality score</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_quality.py --version]]></version_command> 12 <version_command><![CDATA[read_quality.py --version]]></version_command>
17 13
18 <command><![CDATA[ 14 <command><![CDATA[
19 read_quality.py 15 read_quality.py
20 --input-file $input 16 --input-file '${input}'
21 --out-prefix output 17 --out-prefix output
22 -r $reduce 18 -r ${reduce}
23 --mapq $mapq 19 --mapq ${mapq}
24 ]]> 20 ]]>
25 </command> 21 </command>
26 22
27 <inputs> 23 <inputs>
28 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/> 24 <expand macro="bam_sam_param" />
29 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/> 25 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/>
30 <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" /> 26 <expand macro="mapq_param" />
27 <expand macro="rscript_output_param" />
31 </inputs> 28 </inputs>
32 29
33 <outputs> 30 <outputs>
34 <data format="txt" name="outputr" from_work_dir="output.qual.r" label="${tool.name} on ${on_string} (R Script)" /> 31 <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap pdf)" />
35 <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap PDF)" /> 32 <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot pdf)" />
36 <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot PDF)" /> 33 <expand macro="rscript_output_data" filename="output.qual.r" />
37 </outputs> 34 </outputs>
38 35
39 <tests> 36 <tests>
40 <test> 37 <test>
41 <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/> 38 <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
39 <param name="rscript_output" value="true" />
42 <output name="outputr" file="output.qual.r"/> 40 <output name="outputr" file="output.qual.r"/>
41 <output name="outputheatpdf" file="output.qual.heatmap.pdf" compare="sim_size" />
42 <output name="outputboxpdf" file="output.qual.boxplot.pdf" compare="sim_size" />
43 </test> 43 </test>
44 </tests> 44 </tests>
45 45
46 <help><![CDATA[ 46 <help><![CDATA[
47 read_quality.py 47 read_quality.py
68 Output 68 Output
69 ++++++++++++++ 69 ++++++++++++++
70 70
71 1. output.qual.r 71 1. output.qual.r
72 2. output.qual.boxplot.pdf 72 2. output.qual.boxplot.pdf
73 .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.plot.png 73 .. image:: $PATH_TO_IMAGES/36mer.qual.plot.png
74 :height: 600 px 74 :height: 600 px
75 :width: 600 px 75 :width: 600 px
76 :scale: 80 % 76 :scale: 80 %
77 3. output.qual.heatmap.pdf 77 3. output.qual.heatmap.pdf
78 .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.heatmap.png 78 .. image:: $PATH_TO_IMAGES/36mer.qual.heatmap.png
79 :height: 600 px 79 :height: 600 px
80 :width: 600 px 80 :width: 600 px
81 :scale: 80 % 81 :scale: 80 %
82 82
83 Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density") 83 Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density")
84 84
85 ----- 85 @ABOUT@
86 86
87 About RSeQC
88 +++++++++++
89
90 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.
91
92 The RSeQC package is licensed under the GNU GPL v3 license.
93
94 .. image:: http://rseqc.sourceforge.net/_static/logo.png
95
96 .. _RSeQC: http://rseqc.sourceforge.net/
97 ]]> 87 ]]>
98 </help> 88 </help>
99 89
100 <expand macro="citations" /> 90 <expand macro="citations" />
101 91