Mercurial > repos > nilesh > rseqc

comparison read_quality.xml @ 63:27e16a30667a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 5968573462fa
children
comparison
equal deleted inserted replaced
62:473382134e56 63:27e16a30667a
9 Required due to conda solver bug: https://github.com/conda/conda/issues/6269 9 Required due to conda solver bug: https://github.com/conda/conda/issues/6269
10 See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info 10 See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info
11 --> 11 -->
12 <requirement type="package" version="4.2.2">r-base</requirement> 12 <requirement type="package" version="4.2.2">r-base</requirement>
13 </expand> 13 </expand>
14 14 <expand macro="stdio"/>
15 <expand macro="stdio" />
16
17 <version_command><![CDATA[read_quality.py --version]]></version_command> 15 <version_command><![CDATA[read_quality.py --version]]></version_command>
18
19 <command><![CDATA[ 16 <command><![CDATA[
20 @BAM_SAM_INPUTS@ 17 @BAM_SAM_INPUTS@
21 read_quality.py 18 read_quality.py
22 --input-file 'input.${extension}' 19 --input-file 'input.${extension}'
23 --out-prefix output 20 --out-prefix output
24 -r ${reduce} 21 -r ${reduce}
25 --mapq ${mapq} 22 --mapq ${mapq}
26 ]]> 23 ]]>
27 </command> 24 </command>
28
29 <inputs> 25 <inputs>
30 <expand macro="bam_sam_param" /> 26 <expand macro="bam_sam_param"/>
31 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/> 27 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/>
32 <expand macro="mapq_param" /> 28 <expand macro="mapq_param"/>
33 <expand macro="rscript_output_param" /> 29 <expand macro="rscript_output_param"/>
34 </inputs> 30 </inputs>
35
36 <outputs> 31 <outputs>
37 <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap pdf)" /> 32 <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap pdf)"/>
38 <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot pdf)" /> 33 <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot pdf)"/>
39 <expand macro="rscript_output_data" filename="output.qual.r" /> 34 <expand macro="rscript_output_data" filename="output.qual.r"/>
40 </outputs> 35 </outputs>
41
42 <tests> 36 <tests>
43 <test> 37 <test expect_num_outputs="3">
44 <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/> 38 <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
45 <param name="rscript_output" value="true" /> 39 <param name="rscript_output" value="true"/>
46 <output name="outputr" file="output.qual_r"/> 40 <output name="outputr" file="output.qual_r"/>
47 <output name="outputheatpdf" file="output.qual.heatmap.pdf" compare="sim_size" /> 41 <output name="outputheatpdf" file="output.qual.heatmap.pdf" compare="sim_size"/>
48 <output name="outputboxpdf" file="output.qual.boxplot.pdf" compare="sim_size" /> 42 <output name="outputboxpdf" file="output.qual.boxplot.pdf" compare="sim_size"/>
49 </test> 43 </test>
50 </tests> 44 </tests>
51
52 <help><![CDATA[ 45 <help><![CDATA[
53 read_quality.py 46 read_quality.py
54 +++++++++++++++ 47 +++++++++++++++
55 48
56 According to SAM specification, if Q is the character to represent "base calling quality" 49 According to SAM specification, if Q is the character to represent "base calling quality"
90 83
91 @ABOUT@ 84 @ABOUT@
92 85
93 ]]> 86 ]]>
94 </help> 87 </help>
95 88 <expand macro="citations"/>
96 <expand macro="citations" />
97
98 </tool> 89 </tool>