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comparison metilene.xml @ 6:f9883968b113 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/metilene commit 090bc9bb5c775600f4727d8729a032b52e78bd05-dirty
author rnateam
date Thu, 17 Dec 2015 17:09:39 -0500
parents b6263bd3666f
children 9ad744d0804b
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5:b6263bd3666f 6:f9883968b113
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="metilene" name="metilene" version="0.2-4.4"> 2 <tool id="metilene" name="metilene" version="0.2-4.0">
3 <description> 3 <description>
4 calling differentially methylated regions from 4 calling differentially methylated regions from bisulfite sequencing data
5 bisulfite sequencing data
6 </description> 5 </description>
7
8 <requirements> 6 <requirements>
9 <requirement type="binary">Rscript</requirement> 7 <requirement type="package" version="0.2-4">metilene</requirement>
10 <requirement type="package" version="5.18.1" >perl</requirement> 8 <requirement type="package" version="5.18.1">perl</requirement>
11 <requirement type="package" version="3.2.1" >R</requirement> 9 <requirement type="package" version="3.2.1">R</requirement>
12 <requirement type="package" version="2.24" >bedtools</requirement> 10 <requirement type="package" version="0.9.3">r_ggplot2</requirement>
13 <requirement type="package" version="0.2-4" >metilene</requirement> 11 <requirement type="package" version="2.24">bedtools</requirement>
14 <requirement type="package" version="8.22">gnu_coreutils</requirement> 12 <requirement type="package" version="8.22">gnu_coreutils</requirement>
15 </requirements> 13 </requirements>
16
17 <stdio> 14 <stdio>
18 <exit_code range=":-1"/> 15 <exit_code range=":-1"/>
19 <exit_code range="1:" /> 16 <exit_code range="1:" />
20 </stdio> 17 </stdio>
21
22 <version_command>echo "0.2-4"</version_command> 18 <version_command>echo "0.2-4"</version_command>
23
24 <command><![CDATA[ 19 <command><![CDATA[
25 ## =============== preprocessing 20 ## preprocessing
26 ## generate metilene_g1_g2.input from multiple bedgraph files 21 ## generate metilene_g1_g2.input from multiple bedgraph files
27 metilene_input.pl 22 metilene_input.pl
28 --in1 $opt_in1 23 --in1 $opt_in1
29 ##echo ",".join(map(str,$opt_in1)) 24 --in2 $opt_in2
30 --in2 $opt_in2 25 >/dev/null 2>/dev/null
31 ##echo ",".join(map(str,$opt_in2)) 26 &&
32 >/dev/null 2>/dev/null 27 ## metilene main program
33 ; 28 metilene
34 ## =============== metilene main program 29 -M $Options.opt_M
35 metilene 30 -m $Options.opt_m
36 -M $Options.opt_M -m $Options.opt_m -d $Options.opt_d -t 1 -f 1 -v $Options.opt_v 31 -d $Options.opt_d
37 metilene_g1_g2.input 32 -t 1
38 >$output_bedlike 33 -f 1
39 2>/dev/null 34 -v $Options.opt_v
40 ; 35 metilene_g1_g2.input
41 ## =============== postprocessing 36 >$output_bedlike
37 2>/dev/null
38 &&
39 ## postprocessing
42 cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null 40 cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null
43 ; 41 &&
44 ## write to job directory ... 42 ## write to job directory
45 metilene_output.pl -q $output_bedlike -p 0.05 -o ./metilene >/dev/null 2>/dev/null 43 metilene_output.pl
46 ; 44 -q $output_bedlike
47 ## ... and move to output files 45 -p 0.05
48 mv metilene_qval.0.05.bedgraph $output_qval_bedgraph 2>/dev/null; 46 -o ./metilene >/dev/null 2>/dev/null
49 mv metilene_qval.0.05.out $output_qval_out 2>/dev/null;
50 mv metilene_qval.0.05.pdf $output_qval_pdf 2>/dev/null
51 ]]></command> 47 ]]></command>
52
53 <inputs> 48 <inputs>
54 <!-- input bedgraph files 1 --> 49 <!-- input bedgraph files 1 -->
55 <param 50 <param name="opt_in1" type="data" format="bed,bedgraph" multiple="true"
56 name="opt_in1"
57 type="data" format="bed,bedgraph" multiple="true"
58 optional="false"
59 label="Input group 1" 51 label="Input group 1"
60 help="set of sorted bedgraph input profiles of group 1" /> 52 help="set of sorted bedgraph input profiles of group 1" />
61 <!-- input bedgraph files 2 --> 53 <!-- input bedgraph files 2 -->
62 <param 54 <param name="opt_in2" type="data" format="bed,bedgraph" multiple="true"
63 name="opt_in2"
64 type="data" format="bed,bedgraph" multiple="true"
65 optional="false"
66 label="Input group 2" 55 label="Input group 2"
67 help="set of sorted bedgraph input profiles of group 2" /> 56 help="set of sorted bedgraph input profiles of group 2" />
68 57
69 <!-- Advanced parameters (folded) --> 58 <!-- Advanced parameters (folded) -->
70 <section name="Options" title="Advanced Options" expanded="False"> 59 <section name="Options" title="Advanced Options" expanded="False">
71 <param 60 <param name="opt_M" type="integer" value="300"
72 name="opt_M"
73 label="The allowed nt distance between two CpGs within a DMR" 61 label="The allowed nt distance between two CpGs within a DMR"
74 type="integer" 62 help="-M, --maxdist"/>
75 optional="false"
76 value="300"
77 help="-M, --maxdist"/>
78 63
79 <param 64 <param name="opt_m" type="integer" value="10"
80 name="opt_m"
81 label="The minimum # of CpGs in a DMR" 65 label="The minimum # of CpGs in a DMR"
82 type="integer" 66 help="-m, --mincpgs"/>
83 optional="false" 67
84 value="10" 68 <param name="opt_d" type="float" value="0.1"
85 help="-m, --mincpgs"/>
86
87 <param
88 name="opt_d"
89 label="The minimum mean methylation difference for calling DMRs" 69 label="The minimum mean methylation difference for calling DMRs"
90 type="float" 70 help="-d, --minMethDiff"/>
91 optional="false"
92 value="0.1"
93 help="-d, --minMethDiff"/>
94 71
95 <param 72 <param name="opt_v" type="float" value="0.7" label="Stringency of the valley filter (0.0 - 1.0)"
96 name="opt_v" 73 help="-v, --valley">
97 label="Stringency of the valley filter (0.0 - 1.0)" 74 <validator type="in_range" min="0.0" max="1.0" message="Valley filter value must be in [0,1]." />
98 type="float" 75 </param>
99 optional="false" 76 </section>
100 value="0.7"
101 help="-v, --valley">
102 <validator type="in_range" min="0.0" max="1.0"
103 message="Valley filter value must be in [0,1]." />
104 </param>
105 </section>
106 </inputs> 77 </inputs>
107
108 <outputs> 78 <outputs>
109 <!-- finally: for bed-like use format=tabular --> 79 <!-- finally: for bed-like use format=tabular -->
110 <data format="tabular" name="output_bedlike" 80 <data format="tabular" name="output_bedlike"
111 label="${tool.name} on ${on_string}" /> 81 label="${tool.name} on ${on_string}" />
112 <data format="bedgraph" name="output_bedgraph" 82 <data format="bedgraph" name="output_bedgraph"
113 label="${tool.name} on ${on_string}" /> 83 label="${tool.name} bedgraph on ${on_string}" />
114 <data format="bedgraph" name="output_qval_bedgraph" 84 <data format="bedgraph" name="output_qval_bedgraph"
115 label="${tool.name} qval&lt;0.05 bedgraph on ${on_string}" /> 85 label="${tool.name} qval&lt;0.05 bedgraph on ${on_string}"
86 from_work_dir="metilene_qval.0.05.bedgraph" />
116 <data format="pdf" name="output_qval_pdf" 87 <data format="pdf" name="output_qval_pdf"
117 label="${tool.name} qval&lt;0.05 plots on ${on_string}" /> 88 label="${tool.name} qval&lt;0.05 plots on ${on_string}"
89 from_work_dir="metilene_qval.0.05.pdf" />
118 <data format="bedgraph" name="output_qval_out" 90 <data format="bedgraph" name="output_qval_out"
119 label="${tool.name} qval&lt;0.05 out on ${on_string}" /> 91 label="${tool.name} qval&lt;0.05 out on ${on_string}"
92 from_work_dir="metilene_qval.0.05.out" />
120 </outputs> 93 </outputs>
121
122 <tests> 94 <tests>
123 <test> 95 <test>
124 <param name="opt_in1" value="example_S1.bedgraph,example_S2.bedgraph,example_S3.bedgraph,example_S4.bedgraph" /> 96 <param name="opt_in1" value="example_S1.bedgraph,example_S2.bedgraph,example_S3.bedgraph,example_S4.bedgraph" />
125 <param name="opt_in2" value="example_S5.bedgraph,example_S6.bedgraph,example_S7.bedgraph,example_S8.bedgraph" /> 97 <param name="opt_in2" value="example_S5.bedgraph,example_S6.bedgraph,example_S7.bedgraph,example_S8.bedgraph" />
126 <output name="output_bedlike" file="metilene.out" /> 98 <output name="output_bedlike" file="metilene.out" />
127 </test> 99 </test>
128 </tests> 100 </tests>
129
130
131 <help><![CDATA[ 101 <help><![CDATA[
132 **Fast and sensitive calling of differentially methylated regions 102 **Fast and sensitive calling of differentially methylated regions
133 from bisulfite sequencing data** 103 from bisulfite sequencing data**
134 104
135 Detailed documentation of the stand-alone tool metilene is available at 105 Detailed documentation of the stand-alone tool metilene is available at
139 .. __: http://www.bioinf.uni-leipzig.de/Software/metilene/ 109 .. __: http://www.bioinf.uni-leipzig.de/Software/metilene/
140 ]]></help> 110 ]]></help>
141 111
142 <citations> 112 <citations>
143 <citation type="bibtex">@Article{Juhling_Kretzmer_Bernhart-metil_Fast_and-2015, 113 <citation type="bibtex">@Article{Juhling_Kretzmer_Bernhart-metil_Fast_and-2015,
144 author = {Juhling, Frank and Kretzmer, Helene and Bernhart, Stephan 114 author = {Juhling, Frank and Kretzmer, Helene and Bernhart, Stephan
145 H. and Otto, Christian and Stadler, Peter F. and Hoffmann, 115 H. and Otto, Christian and Stadler, Peter F. and Hoffmann,
146 Steve}, 116 Steve},
147 title = {metilene: {Fast} and sensitive calling of differentially 117 title = {metilene: {Fast} and sensitive calling of differentially
148 methylated regions from bisulfite sequencing data}, 118 methylated regions from bisulfite sequencing data},
149 page = {[Epub ahead of print]}, 119 page = {[Epub ahead of print]},
150 journal = {Genome Res}, 120 journal = {Genome Res},
151 year = {2015}, 121 year = {2015},
152 pmid = {26631489}, 122 pmid = {26631489},
153 doi = {10.1101/gr.196394.115}, 123 doi = {10.1101/gr.196394.115},
154 issn = {1088-9051}, 124 issn = {1088-9051},
155 issn = {1549-5469}}</citation> 125 issn = {1549-5469}}</citation>
156 </citations> 126 </citations>
157
158 </tool> 127 </tool>