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comparison FPKM_count.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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equal deleted inserted replaced
62:473382134e56 63:27e16a30667a
1 <tool id="rseqc_FPKM_count" name="FPKM Count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> 1 <tool id="rseqc_FPKM_count" name="FPKM Count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description>calculates raw read count, FPM, and FPKM for each gene</description> 2 <description>calculates raw read count, FPM, and FPKM for each gene</description>
3 <macros> 3 <macros>
4 <import>rseqc_macros.xml</import> 4 <import>rseqc_macros.xml</import>
5 </macros> 5 </macros>
6
7 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
8 7 <expand macro="requirements"/>
9 <expand macro="requirements" /> 8 <expand macro="stdio"/>
10
11 <expand macro="stdio" />
12
13 <version_command><![CDATA[FPKM_count.py --version]]></version_command> 9 <version_command><![CDATA[FPKM_count.py --version]]></version_command>
14
15 <command><![CDATA[ 10 <command><![CDATA[
16 @BAM_SAM_INPUTS@ 11 @BAM_SAM_INPUTS@
17 FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}' 12 FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}'
18 #if str($strand_type.strand_specific) == "pair" 13 #if str($strand_type.strand_specific) == "pair"
19 -d 14 -d
34 @MULTIHITS@ 29 @MULTIHITS@
35 $onlyexonic 30 $onlyexonic
36 --single-read="${singleread}" 31 --single-read="${singleread}"
37 ]]> 32 ]]>
38 </command> 33 </command>
39
40 <inputs> 34 <inputs>
41 <expand macro="bam_param" /> 35 <expand macro="bam_param"/>
42 <expand macro="refgene_param" /> 36 <expand macro="refgene_param"/>
43 <expand macro="strand_type_param" /> 37 <expand macro="strand_type_param"/>
44 <expand macro="multihits_param" /> 38 <expand macro="multihits_param"/>
45 <param name="onlyexonic" type="boolean" value="false" truevalue="--only-exonic" falsevalue="" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" help="(--only-exonic)"/> 39 <param name="onlyexonic" type="boolean" value="false" truevalue="--only-exonic" falsevalue="" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" help="(--only-exonic)"/>
46 <param name="singleread" type="select" label="How should read-pairs that only have one end mapped be counted?" help="(--single-read)"> 40 <param name="singleread" type="select" label="How should read-pairs that only have one end mapped be counted?" help="(--single-read)">
47 <option value="1" selected="true">Treat it as a whole fragment (1)</option> 41 <option value="1" selected="true">Treat it as a whole fragment (1)</option>
48 <option value="0.5">Treat it as a half fragment (0.5)</option> 42 <option value="0.5">Treat it as a half fragment (0.5)</option>
49 <option value="0">Ignore it (0)</option> 43 <option value="0">Ignore it (0)</option>
50 </param> 44 </param>
51 </inputs> 45 </inputs>
52
53 <outputs> 46 <outputs>
54 <data format="tabular" name="output" from_work_dir="output.FPKM.xls" label="${tool.name} on ${on_string}: FPKM counts"/> 47 <data format="tabular" name="output" from_work_dir="output.FPKM.xls" label="${tool.name} on ${on_string}: FPKM counts"/>
55 </outputs> 48 </outputs>
56
57 <tests> 49 <tests>
58 <test> 50 <test expect_num_outputs="1">
59 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 51 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
60 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> 52 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
61 <output name="output" file="output01.tab"/> 53 <output name="output" file="output01.tab"/>
62 </test> 54 </test>
63 <test> 55 <test expect_num_outputs="1">
64 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 56 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
65 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> 57 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
66 <conditional name="multihits_type"> 58 <conditional name="multihits_type">
67 <param name="multihits_type_selector" value="skip_multihits"/> 59 <param name="multihits_type_selector" value="skip_multihits"/>
68 <param name="mapq" value="20"/> 60 <param name="mapq" value="20"/>
69 </conditional> 61 </conditional>
70 <output name="output" file="output02.tab"/> 62 <output name="output" file="output02.tab"/>
71 <assert_command> 63 <assert_command>
72 <has_text text="--mapq=20" /> 64 <has_text text="--mapq=20"/>
73 </assert_command> 65 </assert_command>
74 </test> 66 </test>
75 </tests> 67 </tests>
76
77 <help><![CDATA[ 68 <help><![CDATA[
78 FPKM_count.py 69 FPKM_count.py
79 +++++++++++++ 70 +++++++++++++
80 71
81 Given a BAM file and reference gene model, this program will calculate the raw 72 Given a BAM file and reference gene model, this program will calculate the raw
132 123
133 @ABOUT@ 124 @ABOUT@
134 125
135 ]]> 126 ]]>
136 </help> 127 </help>
137 128 <expand macro="citations"/>
138 <expand macro="citations" />
139
140 </tool> 129 </tool>