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comparison dexseq_count.xml @ 7:469c0d7489bd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
author iuc
date Sun, 29 Jan 2017 06:59:23 -0500
parents 28a2181df3b9
children 0ccbed58b270
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6:e8ca8941952a 7:469c0d7489bd
1 <tool id="dexseq_count" name="DEXSeq-Count" version="1.0"> 1 <tool id="dexseq_count" name="DEXSeq-Count" version="1.20.1">
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 <requirements> 3 <requirements>
4 <requirement type="package" version="1.14">dexseq</requirement> 4 <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement>
5 <requirement type="package" version="0.6.1">htseq</requirement> 5 <requirement type="package" version="0.6.1.post1">htseq</requirement>
6 <requirement type="package" version="0.7.7">pysam</requirement>
7 </requirements> 6 </requirements>
8 <stdio> 7 <stdio>
9 <!-- Anything other than zero is an error --> 8 <!-- Anything other than zero is an error -->
10 <exit_code range="1:" /> 9 <exit_code range="1:" />
11 <exit_code range=":-1" /> 10 <exit_code range=":-1" />
14 <regex match="Exception:" /> 13 <regex match="Exception:" />
15 </stdio> 14 </stdio>
16 <command> 15 <command>
17 <![CDATA[ 16 <![CDATA[
18 #if $mode.mode_select == "prepare": 17 #if $mode.mode_select == "prepare":
19 python \$DEXSEQ_ROOT/python_scripts/dexseq_prepare_annotation.py 18 dexseq_prepare_annotation.py
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 python \$DEXSEQ_ROOT/python_scripts/dexseq_count.py 23 dexseq_count.py
25 -f bam 24 -f bam
26 -p $mode.paired 25 -p $mode.paired
27 -s $mode.stranded 26 -s $mode.stranded
28 -a $mode.qual 27 -a $mode.qual
29 -r $mode.order 28 -r $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 ]]> 33 ]]>
35 </command> 34 </command>
36 <inputs> 35 <inputs>
37 <conditional name="mode"> 36 <conditional name="mode">
40 <option value="count">Count reads</option> 39 <option value="count">Count reads</option>
41 </param> 40 </param>
42 <when value="prepare"> 41 <when value="prepare">
43 <param name="gtffile" type="data" format="gff" label="GTF file"/> 42 <param name="gtffile" type="data" format="gff" label="GTF file"/>
44 <param name="aggregate" type="boolean" checked="True" truevalue="yes" falsevalue="no" 43 <param name="aggregate" type="boolean" checked="True" truevalue="yes" falsevalue="no"
45 label="Aggretare genes with exons?" 44 label="Aggregate 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."/> 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."/>
47 </when> 46 </when>
48 <when value="count"> 47 <when value="count">
49 <param name="bamfile" type="data" format="bam" label="Input bam file"/> 48 <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"/> 49 <param name="flattened_gtf_in" type="data" format="gff" label="DEXSeq compatible GTF file" help="Created by prepare mode"/>
83 82
84 <help> 83 <help>
85 <![CDATA[ 84 <![CDATA[
86 .. class:: infomark 85 .. class:: infomark
87 86
88 **What it does** 87 **What it does**
89 88
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. 89 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 90
92 91
93 **Inputs** 92 **Inputs**