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comparison dapars.xml @ 5:a5d8b08af089 draft

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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
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4:73b932244237 5:a5d8b08af089
1 <tool id="dapars" name="dapars" version="0.1.5"> 1 <tool id="dapars" name="dapars" version="0.2.0">
2 <description>infer de-novo alternative polyadenylation from rna-seq</description> 2 <description>infer de-novo alternative polyadenylation from rna-seq</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.9">numpy</requirement> 4 <requirement type="package" version="1.9">numpy</requirement>
5 <requirement type="package" version="2.22">bedtools</requirement> 5 <requirement type="package" version="0.14">scipy</requirement>
6 <requirement type="package" version="1.4">matplotlib</requirement>
7 <requirement type="package" version="0.7.5">tabulate</requirement>
6 </requirements> 8 </requirements>
7 <stdio> 9 <stdio>
8 <exit_code range="1:" /> 10 <exit_code range="1:" />
9 </stdio> 11 </stdio>
10 <command interpreter="python"><![CDATA[ 12 <command interpreter="python"><![CDATA[
11 dapars.py -c 13 dapars.py -c $controls
12 #for $c in $controls:
13 "$c"
14 #end for
15 -t 14 -t
16 #for $t in $treatments: 15 #for $t in $treatments:
17 "$t" 16 "$t"
18 #end for 17 #end for
19 -u "$utr" 18 -u "$utr"
22 --coverage_threshold "$coverage_threshold" 21 --coverage_threshold "$coverage_threshold"
23 --search_start "$search_start" 22 --search_start "$search_start"
24 #if $make_breakpoint: 23 #if $make_breakpoint:
25 -b "$breakpoint_bed" 24 -b "$breakpoint_bed"
26 #end if 25 #end if
26 #if $make_html:
27 -p "$html_file.files_path"
28 -html "$html_file"
29 #end if
27 ]]></command> 30 ]]></command>
28 <inputs> 31 <inputs>
29 <param type="data" name="utr" format="gtf" label="GFF file containing 3prime UTRs" help="featureType of the UTRs 32 <param type="data" name="utr" format="gtf" label="GFF file containing 3prime UTRs" help="featureType of the UTRs
30 must be UTR, and the attribute group must have geneid in first position."/> 33 must be UTR, and the attribute group must have geneid in first position."/>
31 <param type="data" name="controls" format="bam,sam" multiple="True" label="Control alignment files" help="Select control alignment files" /> 34 <param type="data" name="controls" format="bam,sam" multiple="True" label="Control alignment files" help="Select control alignment files" />
32 <param type="data" name="treatments" format="bam,sam" multiple="True" label="Treatment alignment files" help="Select treatment alignment files" /> 35 <param type="data" name="treatments" format="bam,sam" multiple="True" label="Treatment alignment files" help="Select treatment alignment files" />
33 <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."/> 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."/>
34 <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."/> 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."/>
35 <param name="make_breakpoint" type="boolean" checked="False" label="Output bedfile with breakpoint positions?"/> 38 <param name="make_breakpoint" type="boolean" checked="False" label="Output bedfile with breakpoint positions?"/>
39 <param name="make_html" type="boolean" checked="False" label="Output HTML table with plot for every UTR?"/>
36 </inputs> 40 </inputs>
37 <outputs> 41 <outputs>
38 <data name="apa_sites" format="tabular" /> 42 <data name="apa_sites" format="tabular" />
39 <data name="breakpoint_bed" format="bed6"> 43 <data name="breakpoint_bed" format="bed6">
40 <filter>(make_breakpoint == True)</filter> 44 <filter>(make_breakpoint == True)</filter>
41 </data> 45 </data>
46 <data name="html_file" format="html">
47 <filter>(make_html == True)</filter>
48 </data>
42 </outputs> 49 </outputs>
50 <tests>
51 <test>
52 <param name="utr" value="example.gtf"></param>
53 <param name="controls" value="c1.bam,c2.bam,c3.bam"></param>
54 <param name="treatments" value="t1.bam,t2.bam,t3.bam"></param>
55 <param name="coverage_threshold" value="5"></param>
56 <param name="search_start" value="1"></param>
57 <param name="make_breakpoint" value="True"></param>
58 <param name="make_html" value="True"></param>
59 <output name="apa_sites" file="dapars.tab"></output>
60 <output name="breakpoint_bed" file="breakpoint.bed"></output>
61 </test>
62 </tests>
43 <help><![CDATA[ 63 <help><![CDATA[
44 TODO: Fill in help. 64 DaPars works on RNAseq aligment files to find drops of coverage within UTRs. The coverage is then divided into
65 proximal and distal, and the ratio is calculated for each sample.
45 ]]></help> 66 ]]></help>
46 <citations> 67 <citations>
47 <citation type="doi">10.1038/ncomms6274</citation> 68 <citation type="doi">10.1038/ncomms6274</citation>
48 </citations> 69 </citations>
49 </tool> 70 </tool>