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comparison bam2wig.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
1 <tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> 1 <tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description> 2 <description>
3 converts all types of RNA-seq data from .bam to .wig 3 converts all types of RNA-seq data from BAM to Wiggle
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>rseqc_macros.xml</import> 6 <import>rseqc_macros.xml</import>
7 </macros> 7 </macros>
8
9 <expand macro="bio_tools"/> 8 <expand macro="bio_tools"/>
10 9 <expand macro="requirements"/>
11 <expand macro="requirements" /> 10 <expand macro="stdio"/>
12
13 <expand macro="stdio" />
14
15 <version_command><![CDATA[bam2wig.py --version]]></version_command> 11 <version_command><![CDATA[bam2wig.py --version]]></version_command>
16
17 <command><![CDATA[ 12 <command><![CDATA[
18 @BAM_SAM_INPUTS@ 13 @BAM_SAM_INPUTS@
19 bam2wig.py -i 'input.${extension}' -s '${chromsize}' -o outfile 14 bam2wig.py -i 'input.${extension}' -s '${chromsize}' -o outfile
20 15
21 #if str($strand_type.strand_specific) == "pair" 16 #if str($strand_type.strand_specific) == "pair"
42 37
43 @MULTIHITS@ 38 @MULTIHITS@
44 ]]> 39 ]]>
45 </command> 40 </command>
46 <inputs> 41 <inputs>
47 <expand macro="bam_param" /> 42 <expand macro="bam_param"/>
48 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" help="(--chromSize)"/> 43 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" help="(--chromSize)"/>
49 <expand macro="multihits_param" /> 44 <expand macro="multihits_param"/>
50 <conditional name="wigsum_type"> 45 <conditional name="wigsum_type">
51 <param name="wigsum_type_selector" type="select" label="Normalization"> 46 <param name="wigsum_type_selector" type="select" label="Normalization">
52 <option value="normalize">Normalize to specified sum</option> 47 <option value="normalize">Normalize to specified sum</option>
53 <option value="raw" selected="true">Do not normalize</option> 48 <option value="raw" selected="true">Do not normalize</option>
54 </param> 49 </param>
55 <when value="normalize"> 50 <when value="normalize">
56 <param name="totalwig" value="" type="integer" label="specified wigsum" help="(--wigsum)"/> 51 <param name="totalwig" value="" type="integer" label="specified wigsum" help="(--wigsum)"/>
57 </when> 52 </when>
58 <when value="raw"/> 53 <when value="raw"/>
59 </conditional> 54 </conditional>
60 <expand macro="strand_type_param" /> 55 <expand macro="strand_type_param"/>
61 </inputs> 56 </inputs>
62
63 <outputs> 57 <outputs>
64 <data format="wig" name="output" from_work_dir="outfile.wig"> 58 <data format="wig" name="output" from_work_dir="outfile.wig">
65 <filter>strand_type['strand_specific'] == 'none'</filter> 59 <filter>strand_type['strand_specific'] == 'none'</filter>
66 </data> 60 </data>
67 <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string}: forward reads"> 61 <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string}: forward reads">
69 </data> 63 </data>
70 <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string}: reverse reads"> 64 <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string}: reverse reads">
71 <filter>strand_type['strand_specific'] != 'none'</filter> 65 <filter>strand_type['strand_specific'] != 'none'</filter>
72 </data> 66 </data>
73 </outputs> 67 </outputs>
74
75 <tests> 68 <tests>
76 <test> 69 <test expect_num_outputs="1">
77 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 70 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
78 <param name="chromsize" value="hg19.chrom.sizes"/> 71 <param name="chromsize" value="hg19.chrom.sizes"/>
79 <output name="output" file="testwig.wig"/> 72 <output name="output" file="testwig.wig"/>
80 </test> 73 </test>
81 <test> 74 <test expect_num_outputs="1">
82 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 75 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
83 <param name="chromsize" value="hg19.chrom.sizes"/> 76 <param name="chromsize" value="hg19.chrom.sizes"/>
84 <param name="multihits_type_selector" value="skip_multihits"/> 77 <param name="multihits_type_selector" value="skip_multihits"/>
85 <param name="mapq" value="20"/> 78 <param name="mapq" value="20"/>
86 <output name="output" file="testwig.wig"/> 79 <output name="output" file="testwig.wig"/>
87 </test> 80 </test>
88 <test> 81 <test expect_num_outputs="2">
89 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 82 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
90 <param name="chromsize" value="hg19.chrom.sizes"/> 83 <param name="chromsize" value="hg19.chrom.sizes"/>
91 <param name="strand_specific" value="pair"/> 84 <param name="strand_specific" value="pair"/>
92 <param name="pair_type" value="sd"/> 85 <param name="pair_type" value="sd"/>
93 <output name="outputfwd" file="testwig.Forward.wig"/> 86 <output name="outputfwd" file="testwig.Forward.wig"/>
94 <output name="outputrv" file="testwig.Reverse.wig"/> 87 <output name="outputrv" file="testwig.Reverse.wig"/>
95 </test> 88 </test>
96 <test> 89 <test expect_num_outputs="1">
97 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 90 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
98 <param name="chromsize" value="hg19.chrom.sizes"/> 91 <param name="chromsize" value="hg19.chrom.sizes"/>
99 <param name="wigsum_type_selector" value="normalize"/> 92 <param name="wigsum_type_selector" value="normalize"/>
100 <param name="totalwig" value="100"/> 93 <param name="totalwig" value="100"/>
101 <output name="output" file="testwig_wigsum100.wig"/> 94 <output name="output" file="testwig_wigsum100.wig"/>
102 </test> 95 </test>
103 </tests> 96 </tests>
104
105 <help><![CDATA[ 97 <help><![CDATA[
106 bam2wig.py 98 bam2wig.py
107 ++++++++++ 99 ++++++++++
108 100
109 Visualization is the most straightforward and effective way to QC your RNA-seq 101 Visualization is the most straightforward and effective way to QC your RNA-seq
147 .. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html 139 .. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html
148 .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html 140 .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
149 .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1 141 .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
150 ]]> 142 ]]>
151 </help> 143 </help>
152 144 <expand macro="citations"/>
153 <expand macro="citations" />
154
155 </tool> 145 </tool>