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comparison dexseq_count.xml @ 0:4ca0e679f21e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
author iuc
date Thu, 08 Oct 2015 16:52:01 -0400
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1 <tool id="dexseq_count" name="DEXSeq-Count" version="1.0">
2 <description>Prepare and count exon abundancies from RNA-seq data</description>
3 <requirements>
4 <requirement type="package" version="1.14">dexseq</requirement>
5 <requirement type="package" version="0.6.1">htseq</requirement>
6 <requirement type="package" version="0.7.7">pysam</requirement>
7 </requirements>
8 <stdio>
9 <!-- Anything other than zero is an error -->
10 <exit_code range="1:" />
11 <exit_code range=":-1" />
12 <!-- In case the return code has not been set propery check stderr too -->
13 <regex match="Error:" />
14 <regex match="Exception:" />
15 </stdio>
16 <command>
17 <![CDATA[
18 #if $mode.mode_select == "prepare":
19 python \$DEXSEQ_ROOT/python_scripts/dexseq_prepare_annotation.py
20 -r $mode.aggregate
21 $mode.gtffile
22 $flattened_gtf_out
23 #elif $mode.mode_select == "count":
24 python \$DEXSEQ_ROOT/python_scripts/dexseq_count.py
25 -f bam
26 -p $mode.paired
27 -s $mode.stranded
28 -a $mode.qual
29 -r $mode.order
30 $mode.flattened_gtf_in
31 $mode.bamfile
32 $counts_file
33 #end if
34 ]]>
35 </command>
36 <inputs>
37 <conditional name="mode">
38 <param name="mode_select" type="select" label="Mode of operation">
39 <option value="prepare">Prepare annotation</option>
40 <option value="count">Count reads</option>
41 </param>
42 <when value="prepare">
43 <param name="gtffile" type="data" format="gff" label="GTF file"/>
44 <param name="aggregate" type="boolean" checked="True" truevalue="yes" falsevalue="no"
45 label="Aggretare genes with exons?"
46 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."/>
47 </when>
48 <when value="count">
49 <param name="bamfile" type="data" format="bam" label="Input bam file"/>
50 <param name="flattened_gtf_in" type="data" format="gff" label="DEXSeq compatible GTF file" help="Created by prepare mode"/>
51 <param name="paired" type="boolean" checked="True" truevalue="yes" falsevalue="no" label="Is libray paired end?"/>
52 <param name="stranded" type="select" label="Is library strand specific?">
53 <option value="no">No</option>
54 <option value="yes">Yes</option>
55 <option value="reverse">Yes, but reverse</option>
56 </param>
57 <param name="qual" type="integer" value="10" label="Skip all reads with alignment quality lower than the given minimum value"/>
58 <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">
59 <option value="pos">By position</option>
60 <option value="name">By name</option>
61 </param>
62 </when>
63 </conditional>
64 </inputs>
65
66 <outputs>
67 <data format="tabular" name="counts_file" label="DEXSeq count reads on ${on_string}">
68 <filter>mode['mode_select'] == 'count'</filter>
69 </data>
70 <data format="gtf" name="flattened_gtf_out" label="DEXSeq prepare annotation on ${on_string}">
71 <filter>mode['mode_select'] == 'prepare'</filter>
72 </data>
73 </outputs>
74
75 <tests>
76 <test>
77 <param name="mode_select" value="prepare" />
78 <param name="gtffile" ftype="gff" value="original.gtf"/>
79 <param name="aggregate" value="True"/>
80 <output name="flattened_gtf_out" file="flattened.gtf" ftype="gtf"/>
81 </test>
82 </tests>
83
84 <help>
85 <![CDATA[
86 .. class:: infomark
87
88 **What it does**
89
90 The main goal of this tol is to count the number of reads/fragments per exon of each gene in RNA-seq sample. In addition it also prepares your annotation gtf file compatible for counting.
91
92
93 **Inputs**
94
95 Mode-preprare: Takes a normal gtf file as input. For example from ensembl database.
96 Mode-count: Inputs are flattened gtf file and BAM file. The flattened gtf file can be generated from 'prepare' mode of this tool.
97
98 **Output**
99
100 Mode-preprare: 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.
101 Mode-count: Two column tab-delimeted file with exon ids and their read counts.
102
103 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
104
105 ]]>
106 </help>
107 <citations>
108 <citation type="doi">10.1101/gr.133744.111</citation>
109 </citations>
110 </tool>