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comparison metilene.xml @ 9:af2c31467ca0 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/metilene commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
author rnateam
date Wed, 13 Jul 2016 07:38:51 -0400
parents 48462181c628
children efc829e9f292
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8:48462181c628 9:af2c31467ca0
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="metilene" name="metilene" version="0.2-4.1"> 2 <tool id="metilene" name="metilene" version="0.2.6.0">
3 <description> 3 <description>
4 calling differentially methylated regions from bisulfite sequencing data 4 calling differentially methylated regions from bisulfite sequencing data
5 </description> 5 </description>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="0.2-4">metilene</requirement> 7 <requirement type="package" version="0.2.6">metilene</requirement>
8 <requirement type="package" version="5.18.1">perl</requirement> 8 <requirement type="package" version="5.18.1">perl</requirement>
9 <requirement type="package" version="0.9.3">r_ggplot2</requirement> 9 <!--requirement type="package" version="3.2.1">R</requirement-->
10 <!--requirement type="package" version="0.9.3">r_ggplot2</requirement-->
11
12 <requirement type="package" version="2.0.0">r-ggplot2</requirement>
10 <requirement type="package" version="2.24">bedtools</requirement> 13 <requirement type="package" version="2.24">bedtools</requirement>
11 <requirement type="package" version="8.22">gnu_coreutils</requirement> 14 <requirement type="package" version="8.22">gnu_coreutils</requirement>
12 </requirements> 15 </requirements>
13 <stdio> 16 <stdio>
14 <exit_code range=":-1"/> 17 <exit_code range=":-1"/>
15 <exit_code range="1:" /> 18 <exit_code range="1:" />
16 </stdio> 19 </stdio>
17 <version_command>echo "0.2-4"</version_command> 20 <version_command>echo "0.2.6"</version_command>
18 <command><![CDATA[ 21 <command><![CDATA[
19 ## preprocessing 22 ## preprocessing
20 ## generate metilene_g1_g2.input from multiple bedgraph files 23 ## generate metilene_g1_g2.input from multiple bedgraph files
21 metilene_input.pl 24 metilene_input.pl
22 --in1 "$opt_in1" 25 --in1 "$opt_in1"
23 --in2 "$opt_in2" 26 --in2 "$opt_in2"
24 >/dev/null 2>/dev/null 27 >/dev/null
28 ##2>/dev/null
25 && 29 &&
26 ## metilene main program 30 ## metilene main program
27 metilene 31 metilene
28 -M $Options.opt_M 32 -M $Options.opt_M
29 -m $Options.opt_m 33 -m $Options.opt_m
30 -d $Options.opt_d 34 -d $Options.opt_d
31 -t 1 35 -t \${GALAXY_SLOTS:-4}
32 #if $B: 36 #if $B:
33 -f 2 37 -f 2
34 -B "$B" 38 -B "$B"
35 #else: 39 #else:
36 -f 1 40 -f 1
37 #end if 41 #end if
42 #if $Options.Y:
43 -Y $Options.Y
44 #end if
45 #if $Options.X:
46 -X $Options.X
47 #end if
48
38 -v $Options.opt_v 49 -v $Options.opt_v
39 metilene_g1_g2.input 50 metilene_g1_g2.input
40 > $output_bedlike 51 > $output_bedlike
41 2> /dev/null 52 ##2> /dev/null
42 && 53 &&
43 ## postprocessing 54 ## postprocessing
44 cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null 55 cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null
45 && 56 &&
46 ## write to job directory 57 ## write to job directory
47 metilene_output.pl 58 metilene_output.pl
48 -q $output_bedlike 59 -q $output_bedlike
49 -p 0.05 60 -p 0.05
50 -o ./metilene >/dev/null 2>/dev/null 61 -o ./metilene
62 ##>/dev/null
63 ##2>/dev/null
51 ]]></command> 64 ]]></command>
52 <inputs> 65 <inputs>
53 <!-- input bedgraph files 1 --> 66 <!-- input bedgraph files 1 -->
54 <param name="opt_in1" type="data" format="bed,bedgraph" multiple="true" 67 <param name="opt_in1" type="data" format="bed,bedgraph" multiple="true"
55 label="Input group 1" 68 label="Input group 1"
70 help="-M, --maxdist"/> 83 help="-M, --maxdist"/>
71 84
72 <param name="opt_m" type="integer" value="10" 85 <param name="opt_m" type="integer" value="10"
73 label="The minimum # of CpGs in a DMR" 86 label="The minimum # of CpGs in a DMR"
74 help="-m, --mincpgs"/> 87 help="-m, --mincpgs"/>
88
89 <param argument="X" type="integer" value="" optional="True"
90 label="Specify how many replicates must contain data for a certain CpG position in group 1"
91 help="to estimate missing ones"/>
92
93 <param argument="Y" type="integer" value="" optional="True"
94 label="Specify how many replicates must contain data for a certain CpG position in group 2"
95 help="to estimate missing ones"/>
75 96
76 <param name="opt_d" type="float" value="0.1" 97 <param name="opt_d" type="float" value="0.1"
77 label="The minimum mean methylation difference for calling DMRs" 98 label="The minimum mean methylation difference for calling DMRs"
78 help="-d, --minMethDiff"/> 99 help="-d, --minMethDiff"/>
79 100