Mercurial > repos > mcharles > rapsosnp
comparison rapsodyn/PileupVariant.xml @ 10:0a6c1cfe4dc8 draft
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author | mcharles |
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date | Mon, 19 Jan 2015 04:33:21 -0500 |
parents | 3f7b0788a1c4 |
children |
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9:0e7c6fe60646 | 10:0a6c1cfe4dc8 |
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1 <tool id="PileupVariant" name="PileupVariant" version="1.01"> | 1 <tool id="PileupVariant" name="PileupVariant" version="1.10"> |
2 <description>Keep only mpileup line with variant</description> | 2 <description>Keep only mpileup line with variant</description> |
3 <command interpreter="perl"> | 3 <command interpreter="perl"> |
4 PileupVariant.pl -input_pileup_file $input_pileup_file -log_file $log_file > $output_pileup_file | 4 #if $exclude.do=="YES" |
5 PileupVariant.pl -input_pileup_file $input_pileup_file -input_exclusion_file $input_exclusion_file -log_file $log_file > $output_pileup_file | |
6 #else | |
7 PileupVariant.pl -input_pileup_file $input_pileup_file -log_file $log_file > $output_pileup_file | |
8 #end if | |
9 | |
5 </command> | 10 </command> |
6 <inputs> | 11 <inputs> |
7 <param name="input_pileup_file" type="data" format="pileup" label="Select a suitable input file from your history"/> | 12 <param name="input_pileup_file" type="data" format="pileup" label="Select a suitable input file from your history"/> |
13 <conditional name="exclude"> | |
14 <param name="do" type="select" label="Exclude some position"> | |
15 <option value="NO">NO</option> | |
16 <option value="YES">YES</option> | |
17 </param> | |
18 <when value="YES"> | |
19 <param name="input_exclusion_file" type="data" format="pileup" label="Select a suitable input file from your history"/> | |
20 </when> | |
21 <when value="NO"> | |
22 | |
23 </when> | |
24 </conditional> | |
8 </inputs> | 25 </inputs> |
9 <outputs> | 26 <outputs> |
10 <data name="output_pileup_file" format="pileup" label="${tool.name} on ${on_string}"/> | 27 <data name="output_pileup_file" format="pileup" label="${tool.name} on ${on_string}"/> |
11 <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/> | 28 <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/> |
12 </outputs> | 29 </outputs> |