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comparison dexseq_count.xml @ 4:251393b72616 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
author iuc
date Tue, 11 Dec 2018 00:19:18 -0500
parents f89c9b25feb4
children 2872c633f07e
comparison
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3:f89c9b25feb4 4:251393b72616
2 <description>Prepare and count exon abundancies from RNA-seq data</description> 2 <description>Prepare and count exon abundancies from RNA-seq data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="0.9.1">htseq</requirement>
8 </expand> 7 </expand>
9 <stdio> 8 <stdio>
10 <!-- Anything other than zero is an error --> 9 <!-- Anything other than zero is an error -->
11 <exit_code range="1:" /> 10 <exit_code range="1:" />
12 <exit_code range=":-1" /> 11 <exit_code range=":-1" />
20 -r $mode.aggregate 19 -r $mode.aggregate
21 '$mode.gtffile' 20 '$mode.gtffile'
22 '$flattened_gtf_out' 21 '$flattened_gtf_out'
23 #elif $mode.mode_select == "count": 22 #elif $mode.mode_select == "count":
24 dexseq_count.py 23 dexseq_count.py
25 -f bam 24 --format bam
26 -p $mode.paired 25 --paired $mode.paired
27 -s $mode.stranded 26 --stranded $mode.stranded
28 -a $mode.qual 27 --minaqual $mode.qual
29 -r $mode.order 28 --order $mode.order
30 $mode.flattened_gtf_in 29 $mode.flattened_gtf_in
31 '$mode.bamfile' 30 '$mode.bamfile'
32 '$counts_file' 31 '$counts_file'
33 #end if 32 #end if
34 ]]></command> 33 ]]></command>
45 help="Indicates whether two or more genes sharing an exon should be merged into an 'aggregate gene'. If 'no', the exons that can not be assiged to a single gene are ignored."/> 44 help="Indicates whether two or more genes sharing an exon should be merged into an 'aggregate gene'. If 'no', the exons that can not be assiged to a single gene are ignored."/>
46 </when> 45 </when>
47 <when value="count"> 46 <when value="count">
48 <param name="bamfile" type="data" format="bam" label="Input bam file"/> 47 <param name="bamfile" type="data" format="bam" label="Input bam file"/>
49 <param name="flattened_gtf_in" type="data" format="gff" label="DEXSeq compatible GTF file" help="Created by prepare mode"/> 48 <param name="flattened_gtf_in" type="data" format="gff" label="DEXSeq compatible GTF file" help="Created by prepare mode"/>
50 <param name="paired" type="boolean" checked="True" truevalue="yes" falsevalue="no" label="Is libray paired end?"/> 49 <param name="paired" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Is library paired end?"/>
51 <param name="stranded" type="select" label="Is library strand specific?"> 50 <param name="stranded" type="select" label="Is library strand specific?">
51 <option value="yes" selected="true">Yes</option>
52 <option value="no">No</option> 52 <option value="no">No</option>
53 <option value="yes">Yes</option>
54 <option value="reverse">Yes, but reverse</option> 53 <option value="reverse">Yes, but reverse</option>
55 </param> 54 </param>
56 <param name="qual" type="integer" value="10" label="Skip all reads with alignment quality lower than the given minimum value"/> 55 <param name="qual" type="integer" value="10" label="Skip all reads with alignment quality lower than the given minimum value"/>
57 <param name="order" type="select" label="Sorting order of alignments" help="If you generated your alignments using tophat, they are by default position sorted. Ignored for single-end data"> 56 <param name="order" type="select" label="Sorting order of alignments" help="If you generated your alignments using tophat, they are by default position sorted. Ignored for single-end data">
58 <option value="pos">By position</option> 57 <option value="pos" selected="true">By position</option>
59 <option value="name">By name</option> 58 <option value="name">By name</option>
60 </param> 59 </param>
61 </when> 60 </when>
62 </conditional> 61 </conditional>
63 </inputs> 62 </inputs>
64 63
65 <outputs> 64 <outputs>
66 <data format="tabular" name="counts_file" label="DEXSeq count reads on ${on_string}"> 65 <data name="counts_file" format="tabular" label="DEXSeq count reads on ${on_string}">
67 <filter>mode['mode_select'] == 'count'</filter> 66 <filter>mode['mode_select'] == 'count'</filter>
68 </data> 67 </data>
69 <data format="gtf" name="flattened_gtf_out" label="DEXSeq prepare annotation on ${on_string}"> 68 <data name="flattened_gtf_out" format="gtf" label="DEXSeq prepare annotation on ${on_string}">
70 <filter>mode['mode_select'] == 'prepare'</filter> 69 <filter>mode['mode_select'] == 'prepare'</filter>
71 </data> 70 </data>
72 </outputs> 71 </outputs>
73 72
74 <tests> 73 <tests>
81 <!-- Ensure count mode works --> 80 <!-- Ensure count mode works -->
82 <test> 81 <test>
83 <param name="mode_select" value="count" /> 82 <param name="mode_select" value="count" />
84 <param name="bamfile" ftype="bam" value="in.bam" /> 83 <param name="bamfile" ftype="bam" value="in.bam" />
85 <param name="flattened_gtf_in" ftype="gff" value="flattened.gtf"/> 84 <param name="flattened_gtf_in" ftype="gff" value="flattened.gtf"/>
85 <param name="stranded" value="no" />
86 <output name="counts_file" ftype="tabular" file="out_count.tab"/> 86 <output name="counts_file" ftype="tabular" file="out_count.tab"/>
87 </test> 87 </test>
88 </tests> 88 </tests>
89 89
90 <help><![CDATA[ 90 <help><![CDATA[
95 The main goal of this tool is to count the number of reads/fragments per exon of each gene in RNA-seq samples. In addition, it also prepares your annotation GTF file, making it compatible for counting. 95 The main goal of this tool is to count the number of reads/fragments per exon of each gene in RNA-seq samples. In addition, it also prepares your annotation GTF file, making it compatible for counting.
96 96
97 97
98 **Inputs** 98 **Inputs**
99 99
100 Mode-preprare: Takes a normal gtf file as input. For example from Ensembl database. 100 Mode-preprare: Takes a normal GTF file as input. For example from Ensembl database.
101 Mode-count: Inputs are flattened GTF file and BAM file. The flattened GTF file can be generated from 'prepare' mode of this tool. 101 Mode-count: Inputs are flattened GTF file and BAM file. The flattened GTF file can be generated from 'prepare' mode of this tool.
102 102
103 **Output** 103 **Output**
104 104
105 Mode-prepare: Flattened GTF file that contains only exons with corresponding gene ids from given GTF file. Sometimes two or more genes sharing an exon will be merged into an 'aggregate gene' if the aggregate option was used. 105 Mode-prepare: Flattened GTF file that contains only exons with corresponding gene ids from the input GTF file. Sometimes two or more genes sharing an exon will be merged into an 'aggregate gene' if the aggregate option was used.
106 Mode-count: Two column tab-delimited file with exon ids and their read counts. 106 Mode-count: Two column tab-delimited file with exon ids and their read counts.
107 107
108 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html 108 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
109 109
110 ]]></help> 110 ]]></help>