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

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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 473382134e56
children
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62:473382134e56 63:27e16a30667a
2 <description>determines GC% and read count</description> 2 <description>determines GC% and read count</description>
3 <macros> 3 <macros>
4 <import>rseqc_macros.xml</import> 4 <import>rseqc_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
7 7 <expand macro="requirements"/>
8 <expand macro="requirements" /> 8 <expand macro="stdio"/>
9
10 <expand macro="stdio" />
11
12 <version_command><![CDATA[read_GC.py --version]]></version_command> 9 <version_command><![CDATA[read_GC.py --version]]></version_command>
13
14 <command><![CDATA[ 10 <command><![CDATA[
15 @BAM_SAM_INPUTS@ 11 @BAM_SAM_INPUTS@
16 read_GC.py 12 read_GC.py
17 --input-file 'input.${extension}' 13 --input-file 'input.${extension}'
18 --out-prefix output 14 --out-prefix output
19 --mapq ${mapq} 15 --mapq ${mapq}
20 ]]> 16 ]]>
21 </command> 17 </command>
22
23 <inputs> 18 <inputs>
24 <expand macro="bam_sam_param" /> 19 <expand macro="bam_sam_param"/>
25 <expand macro="mapq_param" /> 20 <expand macro="mapq_param"/>
26 <expand macro="rscript_output_param" /> 21 <expand macro="rscript_output_param"/>
27 </inputs> 22 </inputs>
28
29 <outputs> 23 <outputs>
30 <expand macro="pdf_output_data" filename="output.GC_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/> 24 <expand macro="pdf_output_data" filename="output.GC_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/>
31 <expand macro="xls_output_data" filename="output.GC.xls" label="${tool.name} on ${on_string}: XLS"/> 25 <expand macro="xls_output_data" filename="output.GC.xls" label="${tool.name} on ${on_string}: XLS"/>
32 <expand macro="rscript_output_data" filename="output.GC_plot.r" label="${tool.name} on ${on_string}: Rscript"/> 26 <expand macro="rscript_output_data" filename="output.GC_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
33 </outputs> 27 </outputs>
34
35 <tests> 28 <tests>
36 <test> 29 <test expect_num_outputs="3">
37 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 30 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
38 <param name="rscript_output" value="true" /> 31 <param name="rscript_output" value="true"/>
39 <output name="outputxls" file="output.GC.xls" ftype="tabular"/> 32 <output name="outputxls" file="output.GC.xls" ftype="tabular"/>
40 <output name="outputr" file="output.GC_plot_r" /> 33 <output name="outputr" file="output.GC_plot_r"/>
41 <output name="outputpdf" file="output.GC_plot.pdf" compare="sim_size" /> 34 <output name="outputpdf" file="output.GC_plot.pdf" compare="sim_size"/>
42 </test> 35 </test>
43 </tests> 36 </tests>
44
45 <help><![CDATA[ 37 <help><![CDATA[
46 read_GC.py 38 read_GC.py
47 ++++++++++ 39 ++++++++++
48 40
49 41
67 59
68 @ABOUT@ 60 @ABOUT@
69 61
70 ]]> 62 ]]>
71 </help> 63 </help>
72 64 <expand macro="citations"/>
73 <expand macro="citations" />
74
75 </tool> 65 </tool>