Mercurial > repos > crs4 > edge_pro

annotate edge_pro.xml @ 6:e6e6f5f9b9c4 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
author crs4
date Thu, 31 Aug 2017 12:54:08 -0400
parents d5464c9e1723
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
1 <tool id="edge_pro" name="EDGE-pro" version="1.0.2">
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
2 <description>Gene expression in Prokaryotes</description>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
3 <requirements>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
4 <requirement type="package" version="2.1.0">bowtie2</requirement>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
5 <requirement type="package" version="1.3.1">edge-pro</requirement>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
6 </requirements>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
8 edge.pl -t \${GALAXY_SLOTS:-4} -o edge_out
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
9 ## Mandatory input parameters
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
10 -g '$genome'
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
11 -p '$ptt'
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
12 -r '$rnt'
4
d5464c9e1723 Add support for paired collection of FASTQ (thanks to Inge Alexander Raknes).
crs4
parents: 3
diff changeset
13
6
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
14 #if $singlePaired.sPaired == "single"
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
15 -u '$singlePaired.input1'
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
16 #else if $singlePaired.sPaired == "paired"
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
17 -u '$singlePaired.input1'
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
18 -v '$singlePaired.input2'
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
19 #else if $singlePaired.sPaired == "pairedCollection"
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
20 -u '$singlePaired.input.forward'
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
21 -v '$singlePaired.input.reverse'
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
22 #end if
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
23
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
24 #if $singlePaired.sPaired in ("paired", "pairedCollection")
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
25 #if str($singlePaired.minInsertSize)
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
26 -m $singlePaired.minInsertSize
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
27 #end if
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
28 #if str($singlePaired.maxInsertSize)
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
29 -M $singlePaired.maxInsertSize
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
30 #end if
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
31 #end if
4
d5464c9e1723 Add support for paired collection of FASTQ (thanks to Inge Alexander Raknes).
crs4
parents: 3
diff changeset
32
6
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
33 ## Optional input parameters
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
34 #if $params.settingsType == "full"
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
35 #if str($params.window)
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
36 -w $params.window
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
37 #end if
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
38 #if str($params.utrSize)
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
39 -i $params.utrSize
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
40 #end if
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
41 #if str($params.similarity)
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
42 -x $params.similarity
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
43 #end if
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
44 #if str($params.readLength)
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
45 -l $params.readLength
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
46 #end if
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
47 #if str($params.minCoverage)
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
48 -c $params.minCoverage
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
49 #end if
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
50 #end if
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
51 > '$out_log' 2>&1 ## need to redirect stderr because edge.pl calls bowtie2 and count which write some logging info there
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
52 && cat edge_out.rpkm_* > '$out_rpkm'
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
53 ]]></command>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
54 <inputs>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
55 <conditional name="singlePaired">
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
56 <param name="sPaired" type="select" label="Is this library mate-paired?">
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
57 <option value="single">Single-end</option>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
58 <option value="paired">Paired-end</option>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
59 <option value="pairedCollection">Paired-end collection</option>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
60 </param>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
61 <when value="single">
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
62 <param name="input1" type="data" format="fastqsanger" label="FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)"/>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
63 </when>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
64 <when value="paired">
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
65 <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
66 <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
67 <param name="minInsertSize" argument="-m" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
68 <param name="maxInsertSize" argument="-M" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
69 </when>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
70 <when value="pairedCollection">
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
71 <param name="input" type="data_collection" collection_type="paired" format="fastqsanger" label="FASTQ paired collection" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
72 <param name="minInsertSize" argument="-m" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
73 <param name="maxInsertSize" argument="-M" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
74 </when>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
75 </conditional>
0
7af33315bc5e Uploaded
crs4
parents:
diff changeset
76
6
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
77 <param name="genome" argument="-g" type="data" format="fasta" label="Select the reference genome from your history" help="In FASTA format" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
78 <param name="ptt" argument="-p" type="data" format="ptt" label="Coordinates of coding genes (PTT file)" help="PTT file with coordinates of coding genes" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
79 <param name="rnt" argument="-r" type="data" format="rnt" label="Coordinates of structural RNAs (RNT file)" help="RNT file with coordinates of structural RNA" />
0
7af33315bc5e Uploaded
crs4
parents:
diff changeset
80
6
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
81 <section name="params" title="Advanced parameters" expanded="false">
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
82 <param name="window" argument="-w" type="integer" optional="true" value="100" label="Window length for coverage distribution" help="Used to distribute the coverage between two overlapping genes. See help below for details" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
83 <param name="utrSize" argument="-i" type="integer" optional="true" value="40" label="Size of the untranslated region" help="Enter the size of the untranslated region between the initial transcription site and the start codon" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
84 <param name="similarity" argument="-x" type="float" optional="true" value="0.15" label="Percentage for similar coverage" help="Enter the percentage used to determine when two coverage values are considered similar. See help below for details" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
85 <param name="readLength" argument="-l" type="integer" optional="true" value="" label="Read length" help="If not specified, the first 1000 reads are used to approximate the read length" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
86 <param name="minCoverage" argument="-c" type="integer" optional="true" value="3" label="Minimum average coverage for expressed genes" help="Coverage less than specified is assumed to be noise and gene is considered to not be expressed" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
87 </section>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
88 </inputs>
0
7af33315bc5e Uploaded
crs4
parents:
diff changeset
89
6
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
90 <outputs>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
91 <data name="out_aln" format="sam" label="${tool.name} on ${on_string}: alignment" from_work_dir="edge_out.alignments" />
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
92 <data name="out_rpkm" format="tabular" label="${tool.name} on ${on_string}: rpkm"/>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
93 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log"/>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
94 </outputs>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
95
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
96 <help><![CDATA[
0
7af33315bc5e Uploaded
crs4
parents:
diff changeset
97 **What it does**
7af33315bc5e Uploaded
crs4
parents:
diff changeset
98
7af33315bc5e Uploaded
crs4
parents:
diff changeset
99 `EDGE-pro`_, Estimated Degree of Gene Expression in PROkaryots is an efficient software system to estimate gene expression levels in prokaryotic genomes from RNA-seq data. EDGE-pro uses Bowtie2 for alignment and then estimates expression directly from the alignment results.
7af33315bc5e Uploaded
crs4
parents:
diff changeset
100 EDGE-pro includes routines to assign reads aligning to overlapping gene regions accurately. 15% or more of bacterial genes overlap other genes, making this a significant problem for bacterial RNA-seq, one that is generally ignored by programs designed for eukaryotic RNA-seq experiments.
7af33315bc5e Uploaded
crs4
parents:
diff changeset
101
7af33315bc5e Uploaded
crs4
parents:
diff changeset
102 **Input files:**
7af33315bc5e Uploaded
crs4
parents:
diff changeset
103
7af33315bc5e Uploaded
crs4
parents:
diff changeset
104 .. class:: infomark
7af33315bc5e Uploaded
crs4
parents:
diff changeset
105
7af33315bc5e Uploaded
crs4
parents:
diff changeset
106 Input files with gene coordinates in PTT and RNT format can be retrieved with the Get EDGE-pro Files tool available in Galaxy, or downloaded from the `NCBI ftp repository`_.
7af33315bc5e Uploaded
crs4
parents:
diff changeset
107 This tool accepts files in Sanger FASTQ format (Galaxy *fastqsanger* datatype). Use the FASTQ Groomer tool to prepare your files.
7af33315bc5e Uploaded
crs4
parents:
diff changeset
108
6
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
109 .. _NCBI ftp repository: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/
0
7af33315bc5e Uploaded
crs4
parents:
diff changeset
110
7af33315bc5e Uploaded
crs4
parents:
diff changeset
111 .. class:: warningmark
7af33315bc5e Uploaded
crs4
parents:
diff changeset
112
7af33315bc5e Uploaded
crs4
parents:
diff changeset
113 All 3 types of files (FASTA reference genome, PTT and RNT) must have the same order of chromosomes/plasmids (e.g. if chr1 is before chr2 in genome.fasta file, then chr1 must be before chr2 in ptt and rnt files as well). If there is no PTT or RNT file for one of chromosomes/plasmids, place this chromosome/plasmid at the end of the file.
7af33315bc5e Uploaded
crs4
parents:
diff changeset
114
7af33315bc5e Uploaded
crs4
parents:
diff changeset
115 **License and citation**
7af33315bc5e Uploaded
crs4
parents:
diff changeset
116
3
ddcbf8732706 Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like &#39;Can&#39;t exec &#34;./bowtie2-build&#34;: No such file or directory&#39;). Update Orione citation.
crs4
parents: 2
diff changeset
117 This Galaxy tool is Copyright © 2012-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
0
7af33315bc5e Uploaded
crs4
parents:
diff changeset
118
7af33315bc5e Uploaded
crs4
parents:
diff changeset
119 .. _CRS4 Srl.: http://www.crs4.it/
6
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
120 .. _MIT license: https://opensource.org/licenses/MIT
0
7af33315bc5e Uploaded
crs4
parents:
diff changeset
121
3
ddcbf8732706 Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like &#39;Can&#39;t exec &#34;./bowtie2-build&#34;: No such file or directory&#39;). Update Orione citation.
crs4
parents: 2
diff changeset
122 You can use this tool only if you agree to the license terms of: `EDGE-pro`_.
0
7af33315bc5e Uploaded
crs4
parents:
diff changeset
123
7af33315bc5e Uploaded
crs4
parents:
diff changeset
124 .. _EDGE-pro: http://ccb.jhu.edu/software/EDGE-pro/
6
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
125 ]]></help>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
126 <citations>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
127 <citation type="doi">10.4137/EBO.S11250</citation>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
128 <citation type="doi">10.1093/bioinformatics/btu135</citation>
e6e6f5f9b9c4 planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
crs4
parents: 4
diff changeset
129 </citations>
0
7af33315bc5e Uploaded
crs4
parents:
diff changeset
130 </tool>