annotate dexseq_count.xml @ 8:2872c633f07e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit d6fb005b0dbf26037aab1748d9b5df12876c674d"
author iuc
date Sun, 19 Dec 2021 23:02:46 +0000
parents 251393b72616
children df929f257179
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
2872c633f07e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit d6fb005b0dbf26037aab1748d9b5df12876c674d"
iuc
parents: 4
diff changeset
1 <tool id="dexseq_count" name="DEXSeq-Count" version="@TOOL_VERSION@.1" profile="@PROFILE@">
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
2 <description>Prepare and count exon abundancies from RNA-seq data</description>
8
2872c633f07e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit d6fb005b0dbf26037aab1748d9b5df12876c674d"
iuc
parents: 4
diff changeset
3 <xrefs>
2872c633f07e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit d6fb005b0dbf26037aab1748d9b5df12876c674d"
iuc
parents: 4
diff changeset
4 <xref type="bio.tools">dexseq</xref>
2872c633f07e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit d6fb005b0dbf26037aab1748d9b5df12876c674d"
iuc
parents: 4
diff changeset
5 </xrefs>
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
6 <macros>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
7 <import>macros.xml</import>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
8 </macros>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
9 <expand macro="requirements">
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
10 </expand>
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
11 <stdio>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
12 <!-- Anything other than zero is an error -->
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
13 <exit_code range="1:" />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
14 <exit_code range=":-1" />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
15 <!-- In case the return code has not been set propery check stderr too -->
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
16 <regex match="Error:" />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
17 <regex match="Exception:" />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
18 </stdio>
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
19 <command><![CDATA[
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
20 #if $mode.mode_select == "prepare":
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
21 dexseq_prepare_annotation.py
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
22 -r $mode.aggregate
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
23 '$mode.gtffile'
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
24 '$flattened_gtf_out'
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
25 #elif $mode.mode_select == "count":
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
26 dexseq_count.py
4
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
iuc
parents: 3
diff changeset
27 --format bam
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
iuc
parents: 3
diff changeset
28 --paired $mode.paired
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
iuc
parents: 3
diff changeset
29 --stranded $mode.stranded
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
iuc
parents: 3
diff changeset
30 --minaqual $mode.qual
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
iuc
parents: 3
diff changeset
31 --order $mode.order
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
32 $mode.flattened_gtf_in
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
33 '$mode.bamfile'
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
34 '$counts_file'
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
35 #end if
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
36 ]]></command>
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
37 <inputs>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
38 <conditional name="mode">
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
39 <param name="mode_select" type="select" label="Mode of operation">
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
40 <option value="prepare">Prepare annotation</option>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
41 <option value="count">Count reads</option>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
42 </param>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
43 <when value="prepare">
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
44 <param name="gtffile" type="data" format="gff" label="GTF file"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
45 <param name="aggregate" type="boolean" checked="True" truevalue="yes" falsevalue="no"
1
f1c406f9554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 0
diff changeset
46 label="Aggregate genes with exons?"
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
47 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."/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
48 </when>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
49 <when value="count">
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
50 <param name="bamfile" type="data" format="bam" label="Input bam file"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
51 <param name="flattened_gtf_in" type="data" format="gff" label="DEXSeq compatible GTF file" help="Created by prepare mode"/>
4
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
iuc
parents: 3
diff changeset
52 <param name="paired" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Is library paired end?"/>
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
53 <param name="stranded" type="select" label="Is library strand specific?">
4
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
iuc
parents: 3
diff changeset
54 <option value="yes" selected="true">Yes</option>
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
55 <option value="no">No</option>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
56 <option value="reverse">Yes, but reverse</option>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
57 </param>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
58 <param name="qual" type="integer" value="10" label="Skip all reads with alignment quality lower than the given minimum value"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
59 <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">
4
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
iuc
parents: 3
diff changeset
60 <option value="pos" selected="true">By position</option>
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
61 <option value="name">By name</option>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
62 </param>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
63 </when>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
64 </conditional>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
65 </inputs>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
66
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
67 <outputs>
4
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
iuc
parents: 3
diff changeset
68 <data name="counts_file" format="tabular" label="DEXSeq count reads on ${on_string}">
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
69 <filter>mode['mode_select'] == 'count'</filter>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
70 </data>
4
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
iuc
parents: 3
diff changeset
71 <data name="flattened_gtf_out" format="gtf" label="DEXSeq prepare annotation on ${on_string}">
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
72 <filter>mode['mode_select'] == 'prepare'</filter>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
73 </data>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
74 </outputs>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
75
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
76 <tests>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
77 <test>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
78 <param name="mode_select" value="prepare" />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
79 <param name="gtffile" ftype="gff" value="original.gtf"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
80 <param name="aggregate" value="True"/>
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
81 <output name="flattened_gtf_out" ftype="gtf" compare="sim_size" file="flattened.gtf"/>
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
82 </test>
3
f89c9b25feb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit e785d126b23609208b055fb8902f3b9368e9b839
iuc
parents: 2
diff changeset
83 <!-- Ensure count mode works -->
f89c9b25feb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit e785d126b23609208b055fb8902f3b9368e9b839
iuc
parents: 2
diff changeset
84 <test>
f89c9b25feb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit e785d126b23609208b055fb8902f3b9368e9b839
iuc
parents: 2
diff changeset
85 <param name="mode_select" value="count" />
f89c9b25feb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit e785d126b23609208b055fb8902f3b9368e9b839
iuc
parents: 2
diff changeset
86 <param name="bamfile" ftype="bam" value="in.bam" />
f89c9b25feb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit e785d126b23609208b055fb8902f3b9368e9b839
iuc
parents: 2
diff changeset
87 <param name="flattened_gtf_in" ftype="gff" value="flattened.gtf"/>
4
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
iuc
parents: 3
diff changeset
88 <param name="stranded" value="no" />
3
f89c9b25feb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit e785d126b23609208b055fb8902f3b9368e9b839
iuc
parents: 2
diff changeset
89 <output name="counts_file" ftype="tabular" file="out_count.tab"/>
f89c9b25feb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit e785d126b23609208b055fb8902f3b9368e9b839
iuc
parents: 2
diff changeset
90 </test>
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
91 </tests>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
92
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
93 <help><![CDATA[
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
94 .. class:: infomark
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
95
1
f1c406f9554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 0
diff changeset
96 **What it does**
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
97
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
98 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.
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
99
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
100
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
101 **Inputs**
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
102
4
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
iuc
parents: 3
diff changeset
103 Mode-preprare: Takes a normal GTF file as input. For example from Ensembl database.
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
104 Mode-count: Inputs are flattened GTF file and BAM file. The flattened GTF file can be generated from 'prepare' mode of this tool.
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
105
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
106 **Output**
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
107
4
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
iuc
parents: 3
diff changeset
108 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.
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
109 Mode-count: Two column tab-delimited file with exon ids and their read counts.
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
110
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
111 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
112
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
113 ]]></help>
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
114 <citations>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
115 <citation type="doi">10.1101/gr.133744.111</citation>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
116 </citations>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
117 </tool>