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comparison repmatch_gff3.xml @ 0:d33030c8e2cc draft

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author greg
date Tue, 17 Nov 2015 14:26:08 -0500
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1 <?xml version="1.0"?>
2 <tool id="repmatch_gff3" name="RepMatch" version="@WRAPPER_VERSION@.0">
3 <description>Match paired peaks from two or more replicates</description>
4 <macros>
5 <import>repmatch_gff3_macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>
9 python $__tool_directory__/repmatch_gff3.py
10 #for $i in $input:
11 --input "${i}" "${i.hid}"
12 #end for
13 --method $method
14 --distance $distance
15 --step $step
16 --replicates $replicates
17 --low_limit $low_limit
18 --up_limit $up_limit
19 --output_files $output_files_cond.output_files
20 --output_summary "$output_summary"
21 #if str($output_files_cond.output_files) in ["all", "simple_orphan"]:
22 --output_orphan "$output_orphan"
23 #end if
24 #if str($output_files_cond.output_files) =="all":
25 --plot_format $output_files_cond.plot_format
26 --output_detail "$output_detail"
27 --output_key "$output_key"
28 --output_histogram "$output_histogram"
29 #end if
30 </command>
31 <inputs>
32 <param name="input" type="data" format="gff" multiple="True" min="2" label="Match paired peaks on" />
33 <param name="method" type="select" label="Method of finding match">
34 <option value="closest" selected="True">Closest</option>
35 <option value="largest">Largest</option>
36 <option value="all">All</option>
37 </param>
38 <param name="distance" type="integer" value="50" min="0" label="Maximum distance between peaks in different replicates to allow merging" />
39 <param name="step" type="integer" value="0" min="0" label="Step size" help="Distance for each iteration" />
40 <param name="replicates" type="integer" value="2" min="2" label="Minimum number of replicates that must be matched for merging to occur" />
41 <param name="low_limit" type="integer" value="-1000" label="Lower limit for Crick-Watson distance filter" />
42 <param name="up_limit" type="integer" value="1000" label="Upper limit for Crick-Watson distance filter" />
43 <conditional name="output_files_cond">
44 <param name="output_files" type="select" label="Restrict output to" help="Statistics will always be generated." >
45 <option value="all" selected="True">no restrictions (output everything)</option>
46 <option value="simple">matched pairs only</option>
47 <option value="simple_orphan">matched pairs and orphans only</option>
48 </param>
49 <when value="simple" />
50 <when value="simple_orphan" />
51 <when value="all">
52 <param name="plot_format" type="select" label="Output format for graph">
53 <option value="pdf" selected="True">Pdf</option>
54 <option value="png">Png</option>
55 <option value="svg">Svg</option>
56 </param>
57 </when>
58 </conditional>
59 </inputs>
60 <outputs>
61 <data name="output_summary" format="gff" label="Matched pairs: ${tool.name} on ${on_string}" />
62 <data name="output_orphan" format="tabular" label="Orphans: ${tool.name} on ${on_string}">
63 <filter>output_files_cond["output_files"] in ["all", "simple_orphan"]</filter>
64 </data>
65 <data name="output_detail" format="tabular" label="Details: ${tool.name} on ${on_string}">
66 <filter>output_files_cond["output_files"] == "all"</filter>
67 </data>
68 <data name="output_key" format="tabular" label="Key: ${tool.name} on ${on_string}">
69 <filter>output_files_cond["output_files"] == "all"</filter>
70 </data>
71 <data name="output_histogram" format="pdf" label="Histogram: ${tool.name} on ${on_string}">
72 <filter>output_files_cond["output_files"] == "all"</filter>
73 <actions>
74 <action type="format">
75 <option type="from_param" name="output_files_cond.plot_format" />
76 </action>
77 </actions>
78 </data>
79 </outputs>
80 <tests>
81 <param name="input" value="closest_s_input1.gff" ftype="gff" />
82 <param name="input" value="largest_s_input1.gff" ftype="gff" />
83 <param name="method" value="closest" />
84 <param name="distance" value="50" />
85 <param name="step" value="0" />
86 <param name="replicates" value="2" />
87 <param name="low_limit" value="-1000" />
88 <param name="up_limit" value="1000" />
89 <param name="output_files" value="all" />
90 <param name="plot_format" value="png" />
91 <output name="output_summary" file="summary_out1.gff" ftype="gff" />
92 <output name="output_orphan" file="orphan_out1.tabular" ftype="tabular" />
93 <output name="output_detail" file="orphan_detail1.tabular" ftype="tabular" />
94 <output name="output_key" file="key_out1.tabular" ftype="tabular" />
95 <output name="output_histogram" file="histogram_out1.pdf" ftype="pdf" compare="sim_size" />
96 </tests>
97 <help>
98 **What it does**
99 <![CDATA[
100
101 Replicate matching - matches paired peaks from two or more replicates, and produces a list of matched
102 groups and optionally a list of matched orphans. Additional optional outputs include the median read
103 count for each input, details and a histogram.
104
105 ]]>
106
107 **Options**
108
109 * **Method** - Method to use when calling replicates.
110 * **Distance** - Maximum distance between peaks in different replicates to allow merging.
111 * **Step Size** - Distance for each iteration.
112 * **Replicates** - Minimum number of replicates to call a peak. Number of replicates required must be at least 2.
113 * **Lower Limit** - Lower limit for the Crick-Watson distance filter.
114 * **Upper Limit** - Upper limit for the Crick-Watson distance filter.
115 * **Plot Format** - Output format for graph. The options are PNG or SVG.
116 </help>
117 <expand macro="citations" />
118 </tool>