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comparison rapsodyn/PileupVariant.xml @ 10:0a6c1cfe4dc8 draft

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author mcharles
date Mon, 19 Jan 2015 04:33:21 -0500
parents 3f7b0788a1c4
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9:0e7c6fe60646 10:0a6c1cfe4dc8
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>