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comparison junction_saturation.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 5968573462fa
children
comparison
equal deleted inserted replaced
62:473382134e56 63:27e16a30667a
2 <description>detects splice junctions from each subset and compares them to reference gene model</description> 2 <description>detects splice junctions from each subset and compares them to reference gene model</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 <expand macro="requirements" /> 7 <expand macro="requirements"/>
8 <expand macro="stdio" /> 8 <expand macro="stdio"/>
9 <version_command><![CDATA[junction_saturation.py --version]]></version_command> 9 <version_command><![CDATA[junction_saturation.py --version]]></version_command>
10 <command><![CDATA[ 10 <command><![CDATA[
11 @BAM_SAM_INPUTS@ 11 @BAM_SAM_INPUTS@
12 junction_saturation.py 12 junction_saturation.py
13 --input-file 'input.${extension}' 13 --input-file 'input.${extension}'
21 --percentile-ceiling ${percentiles_type.upBound} 21 --percentile-ceiling ${percentiles_type.upBound}
22 --percentile-step ${percentiles_type.percentileStep} 22 --percentile-step ${percentiles_type.percentileStep}
23 #end if 23 #end if
24 ]]> 24 ]]>
25 </command> 25 </command>
26
27 <inputs> 26 <inputs>
28 <expand macro="bam_sam_param" /> 27 <expand macro="bam_sam_param"/>
29 <expand macro="refgene_param" /> 28 <expand macro="refgene_param"/>
30 <expand macro="min_intron_param" /> 29 <expand macro="min_intron_param"/>
31 <param name="min_coverage" type="integer" label="Minimum number of supporting reads to call a junction (default=1)" value="1" help="(--min-coverage)" /> 30 <param name="min_coverage" type="integer" label="Minimum number of supporting reads to call a junction (default=1)" value="1" help="(--min-coverage)"/>
32 <expand macro="mapq_param" /> 31 <expand macro="mapq_param"/>
33 <conditional name="percentiles_type"> 32 <conditional name="percentiles_type">
34 <param name="percentiles_type_selector" type="select" label="Sampling bounds and frequency"> 33 <param name="percentiles_type_selector" type="select" label="Sampling bounds and frequency">
35 <option value="default" selected="true">Default sampling bounds and frequency</option> 34 <option value="default" selected="true">Default sampling bounds and frequency</option>
36 <option value="specify">Specify sampling bounds and frequency</option> 35 <option value="specify">Specify sampling bounds and frequency</option>
37 </param> 36 </param>
38 <when value="specify"> 37 <when value="specify">
39 <param name="lowBound" type="integer" value="5" label="Lower Bound Sampling Frequency (bp, default=5)" help="(--percentile-floor)"> 38 <param name="lowBound" type="integer" value="5" label="Lower Bound Sampling Frequency (bp, default=5)" help="(--percentile-floor)">
40 <validator type="in_range" min="0" max="100" /> 39 <validator type="in_range" min="0" max="100"/>
41 </param> 40 </param>
42 <param name="upBound" type="integer" value="100" label="Upper Bound Sampling Frequency (bp, default=100)" help="(--percentile-ceiling)"> 41 <param name="upBound" type="integer" value="100" label="Upper Bound Sampling Frequency (bp, default=100)" help="(--percentile-ceiling)">
43 <validator type="in_range" min="0" max="100" /> 42 <validator type="in_range" min="0" max="100"/>
44 </param> 43 </param>
45 <param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" help="(--percentile-step)"> 44 <param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" help="(--percentile-step)">
46 <validator type="in_range" min="0" max="100" /> 45 <validator type="in_range" min="0" max="100"/>
47 </param> 46 </param>
48 </when> 47 </when>
49 <when value="default"/> 48 <when value="default"/>
50 </conditional> 49 </conditional>
51 <expand macro="rscript_output_param" /> 50 <expand macro="rscript_output_param"/>
52 </inputs> 51 </inputs>
53
54 <outputs> 52 <outputs>
55 <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string}: junction saturation (PDF)"/> 53 <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string}: junction saturation (PDF)"/>
56 <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string}: junction saturation (Rscript)"/> 54 <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string}: junction saturation (Rscript)"/>
57 </outputs> 55 </outputs>
58
59 <tests> 56 <tests>
60 <test> 57 <test expect_num_outputs="2">
61 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 58 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
62 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> 59 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
63 <param name="rscript_output" value="true" /> 60 <param name="rscript_output" value="true"/>
64 <output name="outputr" file="output.junctionSaturation_plot_r" compare="sim_size"> 61 <output name="outputr" file="output.junctionSaturation_plot_r" compare="sim_size">
65 <assert_contents> 62 <assert_contents>
66 <has_line line="pdf('output.junctionSaturation_plot.pdf')" /> 63 <has_line line="pdf('output.junctionSaturation_plot.pdf')"/>
67 <has_line line="x=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100)" /> 64 <has_line line="x=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100)"/>
68 </assert_contents> 65 </assert_contents>
69 </output> 66 </output>
70 <output name="outputpdf" file="output.junctionSaturation_plot.pdf" compare="sim_size" /> 67 <output name="outputpdf" file="output.junctionSaturation_plot.pdf" compare="sim_size"/>
71 </test> 68 </test>
72 </tests> 69 </tests>
73
74 <help><![CDATA[ 70 <help><![CDATA[
75 junction_saturation.py 71 junction_saturation.py
76 ++++++++++++++++++++++ 72 ++++++++++++++++++++++
77 73
78 It's very important to check if current sequencing depth is deep enough to perform 74 It's very important to check if current sequencing depth is deep enough to perform
118 114
119 @ABOUT@ 115 @ABOUT@
120 116
121 ]]> 117 ]]>
122 </help> 118 </help>
123 119 <expand macro="citations"/>
124 <expand macro="citations" />
125
126 </tool> 120 </tool>