Mercurial > repos > iuc > repmatch_gff3

comparison repmatch_gff3.xml @ 4:6acaa2c93f47 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9
author iuc
date Wed, 12 Jul 2017 10:11:53 -0400
parents d7f1312b3455
children 7cb4c6424ff8
comparison
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3:f7608d0363bf 4:6acaa2c93f47
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="repmatch_gff3" name="RepMatch" version="@WRAPPER_VERSION@.1"> 2 <tool id="repmatch_gff3" name="RepMatch" version="@WRAPPER_VERSION@.2">
3 <description>Match paired peaks from two or more replicates</description> 3 <description>Match paired peaks from two or more replicates</description>
4 <macros> 4 <macros>
5 <import>repmatch_gff3_macros.xml</import> 5 <import>repmatch_gff3_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <stdio> 8 <command detect_errors="aggressive"><![CDATA[
9 <!-- Anything other than zero is an error --> 9 python '$__tool_directory__/repmatch_gff3.py'
10 <exit_code range=":-1" /> 10 #for $i in $input:
11 <exit_code range="1:" /> 11 --input '${i}' '${i.hid}'
12 <!-- Check stderr in case the return code has not been set --> 12 #end for
13 <regex match="Error:" /> 13 --method $method
14 <regex match="Exception:" /> 14 --distance $distance
15 </stdio> 15 --replicates $replicates
16 <command> 16 --output_files $output_files_cond.output_files
17 python $__tool_directory__/repmatch_gff3.py 17 --output_matched_peaks '$output_matched_peaks'
18 #for $i in $input: 18 #if str($output_files_cond.output_files) in ['all', 'matched_peaks_unmatched_peaks']:
19 --input "${i}" "${i.hid}" 19 --output_unmatched_peaks '$output_unmatched_peaks'
20 #end for 20 #end if
21 --method $method 21 #if str($output_files_cond.output_files) == 'all':
22 --distance $distance 22 --output_detail '$output_detail'
23 --replicates $replicates 23 --output_statistics_table '$output_statistics_table'
24 --output_files $output_files_cond.output_files 24 --output_statistics_histogram '$output_statistics_histogram'
25 --output_matched_peaks "$output_matched_peaks" 25 #end if
26 #if str($output_files_cond.output_files) in ["all", "matched_peaks_unmatched_peaks"]: 26 #if str($advanced_options_cond.advanced_options) == 'on':
27 --output_unmatched_peaks "$output_unmatched_peaks" 27 --step $advanced_options_cond.step
28 #end if 28 --low_limit $advanced_options_cond.low_limit
29 #if str($output_files_cond.output_files) =="all": 29 --up_limit $advanced_options_cond.up_limit
30 --output_detail "$output_detail" 30 #end if
31 --output_statistics_table "$output_statistics_table" 31 ]]></command>
32 --output_statistics_histogram "$output_statistics_histogram"
33 #end if
34 #if str($advanced_options_cond.advanced_options) == "on":
35 --step $advanced_options_cond.step
36 --low_limit $advanced_options_cond.low_limit
37 --up_limit $advanced_options_cond.up_limit
38 #end if
39 </command>
40 <inputs> 32 <inputs>
41 <param name="input" type="data" format="gff" multiple="True" min="2" label="Match paired peaks on" /> 33 <param name="input" type="data" format="gff" multiple="True" min="2" label="Match paired peaks on" />
42 <param name="method" type="select" label="Method of finding match"> 34 <param name="method" type="select" label="Method of finding match">
43 <option value="closest" selected="True">Closest</option> 35 <option value="closest" selected="True">Closest</option>
44 <option value="largest">Largest</option> 36 <option value="largest">Largest</option>