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comparison geneBody_coverage.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
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62:473382134e56 63:27e16a30667a
2 <description>read coverage over gene body</description> 2 <description>read coverage over gene body</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[geneBody_coverage.py --version]]></version_command> 9 <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
10 <command><![CDATA[ 10 <command><![CDATA[
11 #if str($batch_mode.batch_mode_selector) == "merge": 11 #if str($batch_mode.batch_mode_selector) == "merge":
12 #import re 12 #import re
13 #set $input_list = [] 13 #set $input_list = []
28 ln -sf '${batch_mode.input.metadata.bam_index}' '${safename}.bam.bai' && 28 ln -sf '${batch_mode.input.metadata.bam_index}' '${safename}.bam.bai' &&
29 geneBody_coverage.py -i '${safename}.bam' -r '${refgene}' --minimum_length ${minimum_length} -o output 29 geneBody_coverage.py -i '${safename}.bam' -r '${refgene}' --minimum_length ${minimum_length} -o output
30 #end if 30 #end if
31 ]]> 31 ]]>
32 </command> 32 </command>
33 33 <inputs>
34 <inputs> 34 <conditional name="batch_mode">
35 <conditional name="batch_mode"> 35 <param name="batch_mode_selector" type="select" label="Run each sample separately, or combine mutiple samples into one plot">
36 <param name="batch_mode_selector" type="select" label="Run each sample separately, or combine mutiple samples into one plot"> 36 <option value="batch" selected="true">Run each sample separately</option>
37 <option value="batch" selected="true">Run each sample separately</option> 37 <option value="merge">Combine multiple samples into a single plot</option>
38 <option value="merge">Combine multiple samples into a single plot</option> 38 </param>
39 </param> 39 <when value="batch">
40 <when value="batch"> 40 <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/>
41 <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/> 41 </when>
42 </when> 42 <when value="merge">
43 <when value="merge"> 43 <param name="inputs" type="data" label="Input .bam file(s)" format="bam" help="(--input-file)" multiple="true"/>
44 <param name="inputs" type="data" label="Input .bam file(s)" format="bam" help="(--input-file)" multiple="true"/> 44 </when>
45 </when> 45 </conditional>
46 </conditional> 46 <expand macro="refgene_param"/>
47 <expand macro="refgene_param" /> 47 <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length (default: 100)" help="Minimum mRNA length in bp, mRNA that are shorter than this value will be skipped (--minimum_length)."/>
48 <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length (default: 100)" help="Minimum mRNA length in bp, mRNA that are shorter than this value will be skipped (--minimum_length)." /> 48 <expand macro="rscript_output_param"/>
49 <expand macro="rscript_output_param" /> 49 </inputs>
50 </inputs> 50 <outputs>
51 51 <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string}: curves (PDF)"/>
52 <outputs> 52 <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string}: heatmap (PDF)">
53 <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string}: curves (PDF)" /> 53 <filter>batch_mode['batch_mode_selector'] == 'merge' and len(inputs) &gt;= 3</filter>
54 <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string}: heatmap (PDF)"> 54 </data>
55 <filter>batch_mode['batch_mode_selector'] == 'merge' and len(inputs) >= 3</filter> 55 <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" label="${tool.name} on ${on_string}: Rscript"/>
56 </data> 56 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string}: stats (TXT)"/>
57 <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" label="${tool.name} on ${on_string}: Rscript"/> 57 </outputs>
58 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string}: stats (TXT)" /> 58 <!-- PDF Files contain R version, must avoid checking for diff -->
59 </outputs> 59 <tests>
60 60 <test expect_num_outputs="3">
61 <!-- PDF Files contain R version, must avoid checking for diff --> 61 <conditional name="batch_mode">
62 <tests> 62 <param name="batch_mode_selector" value="batch"/>
63 <test> 63 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
64 <conditional name="batch_mode"> 64 </conditional>
65 <param name="batch_mode_selector" value="batch" /> 65 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
66 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 66 <param name="rscript_output" value="true"/>
67 </conditional> 67 <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf" compare="sim_size"/>
68 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" /> 68 <output name="outputr" file="output.geneBodyCoverage_r"/>
69 <param name="rscript_output" value="true" /> 69 <output name="outputtxt" file="output.geneBodyCoverage.txt"/>
70 <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf" compare="sim_size" /> 70 </test>
71 <output name="outputr" file="output.geneBodyCoverage_r" /> 71 <test expect_num_outputs="4">
72 <output name="outputtxt" file="output.geneBodyCoverage.txt" /> 72 <conditional name="batch_mode">
73 </test> 73 <param name="batch_mode_selector" value="merge"/>
74 <test> 74 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
75 <conditional name="batch_mode"> 75 </conditional>
76 <param name="batch_mode_selector" value="merge" /> 76 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
77 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 77 <param name="rscript_output" value="true"/>
78 </conditional> 78 <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf" compare="sim_size"/>
79 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> 79 <output name="outputheatmappdf" file="output2.geneBodyCoverage.heatMap.pdf" compare="sim_size"/>
80 <param name="rscript_output" value="true" /> 80 <output name="outputr" file="output2.geneBodyCoverage_r"/>
81 <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf" compare="sim_size" /> 81 <output name="outputtxt" file="output2.geneBodyCoverage.txt"/>
82 <output name="outputheatmappdf" file="output2.geneBodyCoverage.heatMap.pdf" compare="sim_size" /> 82 </test>
83 <output name="outputr" file="output2.geneBodyCoverage_r" /> 83 </tests>
84 <output name="outputtxt" file="output2.geneBodyCoverage.txt" /> 84 <help><![CDATA[
85 </test>
86
87 </tests>
88
89 <help><![CDATA[
90 ## geneBody_coverage.py 85 ## geneBody_coverage.py
91 86
92 Read coverage over gene body. This module is used to check if read coverage is uniform and if there is any 5\'/3\' bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates plots illustrating the coverage profile along the gene body. 87 Read coverage over gene body. This module is used to check if read coverage is uniform and if there is any 5\'/3\' bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates plots illustrating the coverage profile along the gene body.
93 88
94 If 3 or more BAM files were provided. This program generates a lineGraph and a heatmap. If fewer than 3 BAM files were provided, only lineGraph is generated. See below for examples. 89 If 3 or more BAM files were provided. This program generates a lineGraph and a heatmap. If fewer than 3 BAM files were provided, only lineGraph is generated. See below for examples.
136 131
137 @ABOUT@ 132 @ABOUT@
138 133
139 ]]> 134 ]]>
140 </help> 135 </help>
141 136 <expand macro="citations"/>
142 <expand macro="citations" />
143
144 </tool> 137 </tool>