Mercurial > repos > mvdbeek > dapars

annotate dapars.xml @ 5:a5d8b08af089 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
author mvdbeek
date Thu, 29 Oct 2015 15:51:10 -0400
parents 47b0044bc7f8
children 8a27d7d5fc78
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
1 <tool id="dapars" name="dapars" version="0.2.0">
0
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
2 <description>infer de-novo alternative polyadenylation from rna-seq</description>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
3 <requirements>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
4 <requirement type="package" version="1.9">numpy</requirement>
5
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
5 <requirement type="package" version="0.14">scipy</requirement>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
6 <requirement type="package" version="1.4">matplotlib</requirement>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
7 <requirement type="package" version="0.7.5">tabulate</requirement>
0
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
8 </requirements>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
9 <stdio>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
10 <exit_code range="1:" />
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
11 </stdio>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
12 <command interpreter="python"><![CDATA[
5
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
13 dapars.py -c $controls
0
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
14 -t
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
15 #for $t in $treatments:
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
16 "$t"
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
17 #end for
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
18 -u "$utr"
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
19 -o "$apa_sites"
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
20 -cpu \${GALAXY_SLOTS:-4}
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
21 --coverage_threshold "$coverage_threshold"
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
22 --search_start "$search_start"
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
23 #if $make_breakpoint:
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
24 -b "$breakpoint_bed"
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
25 #end if
5
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
26 #if $make_html:
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
27 -p "$html_file.files_path"
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
28 -html "$html_file"
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
29 #end if
0
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
30 ]]></command>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
31 <inputs>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
32 <param type="data" name="utr" format="gtf" label="GFF file containing 3prime UTRs" help="featureType of the UTRs
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
33 must be UTR, and the attribute group must have geneid in first position."/>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
34 <param type="data" name="controls" format="bam,sam" multiple="True" label="Control alignment files" help="Select control alignment files" />
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
35 <param type="data" name="treatments" format="bam,sam" multiple="True" label="Treatment alignment files" help="Select treatment alignment files" />
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
36 <param type="integer" name="search_start" value="100" optional="False" min="1" label="Search start" help="Search start in nucleotides downstream of the start of the UTR. Necessary to correct for proximal drops in coverage. Select 200 for humans. Genomes with short UTRs may require more prpximal search start points."/>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
37 <param type="float" name="coverage_threshold" value="20" optional="False" label="Coverage threshold" help="Skip the analysis of UTRs whose mean coverage is below the Coverage Threshold in any of the alignment files."/>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
38 <param name="make_breakpoint" type="boolean" checked="False" label="Output bedfile with breakpoint positions?"/>
5
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
39 <param name="make_html" type="boolean" checked="False" label="Output HTML table with plot for every UTR?"/>
0
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
40 </inputs>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
41 <outputs>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
42 <data name="apa_sites" format="tabular" />
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
43 <data name="breakpoint_bed" format="bed6">
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
44 <filter>(make_breakpoint == True)</filter>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
45 </data>
5
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
46 <data name="html_file" format="html">
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
47 <filter>(make_html == True)</filter>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
48 </data>
0
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
49 </outputs>
5
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
50 <tests>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
51 <test>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
52 <param name="utr" value="example.gtf"></param>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
53 <param name="controls" value="c1.bam,c2.bam,c3.bam"></param>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
54 <param name="treatments" value="t1.bam,t2.bam,t3.bam"></param>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
55 <param name="coverage_threshold" value="5"></param>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
56 <param name="search_start" value="1"></param>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
57 <param name="make_breakpoint" value="True"></param>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
58 <param name="make_html" value="True"></param>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
59 <output name="apa_sites" file="dapars.tab"></output>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
60 <output name="breakpoint_bed" file="breakpoint.bed"></output>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
61 </test>
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
62 </tests>
0
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
63 <help><![CDATA[
5
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
64 DaPars works on RNAseq aligment files to find drops of coverage within UTRs. The coverage is then divided into
a5d8b08af089 planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42
mvdbeek
parents: 2
diff changeset
65 proximal and distal, and the ratio is calculated for each sample.
0
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
66 ]]></help>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
67 <citations>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
68 <citation type="doi">10.1038/ncomms6274</citation>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
69 </citations>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
70 </tool>