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comparison metilene.xml @ 7:9ad744d0804b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/metilene commit f332463404ef478e78d3ff4583b806dd68dfd3af-dirty
author rnateam
date Thu, 18 Feb 2016 17:16:49 -0500
parents f9883968b113
children 48462181c628
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6:f9883968b113 7:9ad744d0804b
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="metilene" name="metilene" version="0.2-4.0"> 2 <tool id="metilene" name="metilene" version="0.2-4.1">
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="0.2-4">metilene</requirement>
18 <version_command>echo "0.2-4"</version_command> 18 <version_command>echo "0.2-4"</version_command>
19 <command><![CDATA[ 19 <command><![CDATA[
20 ## preprocessing 20 ## preprocessing
21 ## generate metilene_g1_g2.input from multiple bedgraph files 21 ## generate metilene_g1_g2.input from multiple bedgraph files
22 metilene_input.pl 22 metilene_input.pl
23 --in1 $opt_in1 23 --in1 "$opt_in1"
24 --in2 $opt_in2 24 --in2 "$opt_in2"
25 >/dev/null 2>/dev/null 25 >/dev/null 2>/dev/null
26 && 26 &&
27 ## metilene main program 27 ## metilene main program
28 metilene 28 metilene
29 -M $Options.opt_M 29 -M $Options.opt_M
30 -m $Options.opt_m 30 -m $Options.opt_m
31 -d $Options.opt_d 31 -d $Options.opt_d
32 -t 1 32 -t 1
33 -f 1 33 #if $B:
34 -f 2
35 -B "$B"
36 #else:
37 -f 1
38 #end if
34 -v $Options.opt_v 39 -v $Options.opt_v
35 metilene_g1_g2.input 40 metilene_g1_g2.input
36 >$output_bedlike 41 > $output_bedlike
37 2>/dev/null 42 2> /dev/null
38 && 43 &&
39 ## postprocessing 44 ## postprocessing
40 cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null 45 cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null
41 && 46 &&
42 ## write to job directory 47 ## write to job directory
47 ]]></command> 52 ]]></command>
48 <inputs> 53 <inputs>
49 <!-- input bedgraph files 1 --> 54 <!-- input bedgraph files 1 -->
50 <param name="opt_in1" type="data" format="bed,bedgraph" multiple="true" 55 <param name="opt_in1" type="data" format="bed,bedgraph" multiple="true"
51 label="Input group 1" 56 label="Input group 1"
52 help="set of sorted bedgraph input profiles of group 1" /> 57 help="Set of sorted bedgraph/bed input profiles of group 1" />
53 <!-- input bedgraph files 2 --> 58 <!-- input bedgraph files 2 -->
54 <param name="opt_in2" type="data" format="bed,bedgraph" multiple="true" 59 <param name="opt_in2" type="data" format="bed,bedgraph" multiple="true"
55 label="Input group 2" 60 label="Input group 2"
56 help="set of sorted bedgraph input profiles of group 2" /> 61 help="Set of sorted bedgraph/bed input profiles of group 2" />
57 62
63 <param argument="-B" type="data" format="bed" optional="True"
64 label="BED file containing regions of interest"
65 help="Regions that should be checked for differential methylation." />
66
58 <!-- Advanced parameters (folded) --> 67 <!-- Advanced parameters (folded) -->
59 <section name="Options" title="Advanced Options" expanded="False"> 68 <section name="Options" title="Advanced Options" expanded="False">
60 <param name="opt_M" type="integer" value="300" 69 <param name="opt_M" type="integer" value="300"
61 label="The allowed nt distance between two CpGs within a DMR" 70 label="The allowed nt distance between two CpGs within a DMR"
62 help="-M, --maxdist"/> 71 help="-M, --maxdist"/>