Mercurial > repos > iuc > repmatch_gff3

annotate repmatch_gff3.xml @ 2:d7f1312b3455 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 4eb5632ca7b54134911d40ae94eaf155dc673a71
author iuc
date Fri, 13 Jan 2017 10:27:44 -0500
parents e5c7fffdc078
children 6acaa2c93f47
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
2
d7f1312b3455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 4eb5632ca7b54134911d40ae94eaf155dc673a71
iuc
parents: 1
diff changeset
2 <tool id="repmatch_gff3" name="RepMatch" version="@WRAPPER_VERSION@.1">
0
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
3 <description>Match paired peaks from two or more replicates</description>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
4 <macros>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
5 <import>repmatch_gff3_macros.xml</import>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
6 </macros>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
7 <expand macro="requirements" />
2
d7f1312b3455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 4eb5632ca7b54134911d40ae94eaf155dc673a71
iuc
parents: 1
diff changeset
8 <stdio>
d7f1312b3455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 4eb5632ca7b54134911d40ae94eaf155dc673a71
iuc
parents: 1
diff changeset
9 <!-- Anything other than zero is an error -->
d7f1312b3455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 4eb5632ca7b54134911d40ae94eaf155dc673a71
iuc
parents: 1
diff changeset
10 <exit_code range=":-1" />
d7f1312b3455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 4eb5632ca7b54134911d40ae94eaf155dc673a71
iuc
parents: 1
diff changeset
11 <exit_code range="1:" />
d7f1312b3455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 4eb5632ca7b54134911d40ae94eaf155dc673a71
iuc
parents: 1
diff changeset
12 <!-- Check stderr in case the return code has not been set -->
d7f1312b3455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 4eb5632ca7b54134911d40ae94eaf155dc673a71
iuc
parents: 1
diff changeset
13 <regex match="Error:" />
d7f1312b3455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 4eb5632ca7b54134911d40ae94eaf155dc673a71
iuc
parents: 1
diff changeset
14 <regex match="Exception:" />
d7f1312b3455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 4eb5632ca7b54134911d40ae94eaf155dc673a71
iuc
parents: 1
diff changeset
15 </stdio>
0
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
16 <command>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
17 python $__tool_directory__/repmatch_gff3.py
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
18 #for $i in $input:
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
19 --input "${i}" "${i.hid}"
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
20 #end for
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
21 --method $method
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
22 --distance $distance
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
23 --replicates $replicates
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
24 --output_files $output_files_cond.output_files
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
25 --output_matched_peaks "$output_matched_peaks"
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
26 #if str($output_files_cond.output_files) in ["all", "matched_peaks_unmatched_peaks"]:
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
27 --output_unmatched_peaks "$output_unmatched_peaks"
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
28 #end if
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
29 #if str($output_files_cond.output_files) =="all":
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
30 --output_detail "$output_detail"
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
31 --output_statistics_table "$output_statistics_table"
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
32 --output_statistics_histogram "$output_statistics_histogram"
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
33 #end if
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
34 #if str($advanced_options_cond.advanced_options) == "on":
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
35 --step $advanced_options_cond.step
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
36 --low_limit $advanced_options_cond.low_limit
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
37 --up_limit $advanced_options_cond.up_limit
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
38 #end if
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
39 </command>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
40 <inputs>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
41 <param name="input" type="data" format="gff" multiple="True" min="2" label="Match paired peaks on" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
42 <param name="method" type="select" label="Method of finding match">
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
43 <option value="closest" selected="True">Closest</option>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
44 <option value="largest">Largest</option>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
45 <option value="all">All</option>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
46 </param>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
47 <param name="distance" type="integer" value="50" min="0" label="Maximum distance between peaks in different replicates to allow merging" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
48 <param name="replicates" type="integer" value="2" min="2" label="Minimum number of replicates that must be matched for merging to occur" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
49 <conditional name="output_files_cond">
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
50 <param name="output_files" type="select" label="Select output" help="Statistics will always be generated." >
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
51 <option value="all" selected="True">everything</option>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
52 <option value="matched_peaks">matched paired peaks only</option>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
53 <option value="matched_peaks_unmatched_peaks">matched paired peaks and unmatched paired peaks only</option>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
54 </param>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
55 <when value="matched_peaks" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
56 <when value="matched_peaks_unmatched_peaks" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
57 <when value="all" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
58 </conditional>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
59 <conditional name="advanced_options_cond">
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
60 <param name="advanced_options" type="select" label="Advanced options">
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
61 <option value="off" selected="true">Hide advanced options</option>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
62 <option value="on">Display advanced options</option>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
63 </param>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
64 <when value="on">
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
65 <param name="step" type="integer" value="0" min="0" label="Step size" help="Distance for each iteration" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
66 <param name="low_limit" type="integer" value="-1000" label="Lower limit for Crick-Watson distance filter" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
67 <param name="up_limit" type="integer" value="1000" label="Upper limit for Crick-Watson distance filter" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
68 </when>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
69 <when value="off" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
70 </conditional>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
71 </inputs>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
72 <outputs>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
73 <data name="output_statistics_table" format="tabular" label="Statistics Table: ${tool.name} on ${on_string}">
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
74 <filter>output_files_cond["output_files"] == "all"</filter>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
75 </data>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
76 <data name="output_statistics_histogram" format="pdf" label="Statistics Histogram: ${tool.name} on ${on_string}">
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
77 <filter>output_files_cond["output_files"] == "all"</filter>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
78 </data>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
79 <data name="output_detail" format="tabular" label="Data D: ${tool.name} on ${on_string}">
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
80 <filter>output_files_cond["output_files"] == "all"</filter>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
81 </data>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
82 <data name="output_unmatched_peaks" format="tabular" label="Data UP: ${tool.name} on ${on_string}">
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
83 <filter>output_files_cond["output_files"] in ["all", "matched_peaks_unmatched_peaks"]</filter>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
84 </data>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
85 <data name="output_matched_peaks" format="gff" label="Data MP: ${tool.name} on ${on_string}" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
86 </outputs>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
87 <tests>
1
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
88 <test>
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
89 <param name="input" value="closest_matched_pairs_input1.gff,largest_matched_pairs_input1.gff" ftype="gff" />
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
90 <param name="method" value="closest" />
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
91 <param name="distance" value="50" />
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
92 <param name="replicates" value="2" />
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
93 <param name="output_files" value="all" />
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
94 <param name="step" value="0" />
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
95 <param name="low_limit" value="-1000" />
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
96 <param name="up_limit" value="1000" />
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
97 <output name="output_statistics_table" file="statistics_table_out1.tabular" ftype="tabular" />
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
98 <output name="output_statistics_histogram" file="magic.pdf" ftype="pdf" compare="contains" />
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
99 <output name="output_detail" file="detail_out1.tabular" ftype="tabular" />
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
100 <output name="output_unmatched_peaks" file="unmatched_peaks_out1.tabular" ftype="tabular" />
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
101 <output name="output_matched_peaks" file="matched_peaks_out1.gff" ftype="gff" />
e5c7fffdc078 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
iuc
parents: 0
diff changeset
102 </test>
0
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
103 </tests>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
104 <help>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
105 **What it does**
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
106
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
107 RepMatch accepts two or more input datasets, and starts by defining peak-pair midpoints in the first dataset. It then
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
108 discovers all peak-pair midpoints in the second dataset that are within the distance, defined by the tool's **Maximum
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
109 distance between peaks in different replicates to allow merging** parameter, from the peak-pair midpoint coordinate in
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
110 the first dataset. When encountering multiple candidates to match (one-to-many), RepMatch uses the method defined by
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
111 the tool's **Method of finding match** parameter so that there is at most only a one-to-one match across the two datasets.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
112 This method provides the following options:
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
113
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
114 * **closest** - matches only the closest one in bp distance.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
115 * **largest** - matches the one that contain the most number of reads.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
116 * **all** - both methods are run separately.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
117
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
118 RepMatch matching is an iterative process, as it attempts to find the centroid coordinate amongst all replicates. As such,
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
119 the centroid is the point of reference for "distqnce" and "closest". This process can be sped up by increasing the tool's
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
120 **Step size** parameter.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
121
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
122 The minimum number of replicates that can be matched for a match to occur is defined by the tool's **Minimum number of
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
123 replicates that must be matched for merging to occur** parameter. Additional filters can be applied using the tool's
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
124 **Advanced options**, including a lower and upper limit for the C-W distance.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
125
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
126 .. image:: $PATH_TO_IMAGES/repmatch.png
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
127
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
128 -----
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
129
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
130 **Options**
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
131
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
132 * **Distance** - Maximum distance for discovering all peak-pair midpoints in a second dataset relative to the peak-pair midpoints in the first dataset
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
133 * **Method** - Method to use when encountering multiple candidates to match so that there is at most only a one-to-one match across the two datasets.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
134 * **Step Size** - Distance for each iteration.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
135 * **Replicates** - Minimum number of replicates that can be matched for a match to occur. This value must be at least 2.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
136 * **Lower Limit** - Lower limit for the Crick-Watson distance filter.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
137 * **Upper Limit** - Upper limit for the Crick-Watson distance filter.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
138
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
139 -----
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
140
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
141 **Output Data Files**
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
142
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
143 * **Data MP** - gff file consisting of only peak pairs
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
144
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
145 - Columns are **chr**, **script**, **blank**, **peak start**, **peak end**, **blank**, **normalized tag counts**, **blank** and **info**.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
146 - Peak start and end are separated by one coordinate.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
147 - Normalized tag is the occupancy averaged across replicates.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
148 - Attributes include C-W distance, sum total of tag counts, number of replicates merged.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
149
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
150 * **Data D** - tabular file consisting of the list of all matched replicates.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
151 * **Data UP** - tabular file consisting of all unmatched peak-pairs.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
152
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
153 **Output Statistics Files**
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
154
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
155 * **Statistics Table** - tabular file providing the description key of **Data D**.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
156 * **Statistics Histogram** - graph of the number of matched locations having the indicated replicate counts.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
157
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
158 **Comments on Replicates**
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
159
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
160 Three types of replicates may be considered. Biological replicates represent independently collected biological samples.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
161 At least two biological replicate must be performed for each experiment from which a conclusion is being drawn, and the
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
162 conclusion must be evident in both biological replicates when analyzed separately. Technical replicates represent a re-run
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
163 of the assay on the same biological material. This is usually done when one replicate fails to produce quality data, and is
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
164 used to replace that earlier replicate. Sequencing replicates represent additional sequencing of the same successful library
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
165 in order to obtain more reads should the analysis require it. The reads from individual sequencing replicates are usually
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
166 merged without need for separate analysis.
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
167
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
168 </help>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
169 <expand macro="citations" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
170 </tool>