Mercurial > repos > mcharles > rapsosnp
comparison rapsodyn/PrepareFastqLight.xml @ 8:d857538d9fea draft
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author | mcharles |
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date | Fri, 10 Oct 2014 07:05:36 -0400 |
parents | 3f7b0788a1c4 |
children | 0a6c1cfe4dc8 |
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7:3f7b0788a1c4 | 8:d857538d9fea |
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1 <tool id="PrepareFastqLight" name="PrepareFastqLight" version="1.01"> | 1 <tool id="PrepareFastqLight" name="PrepareFastqLight" version="1.03"> |
2 <description>Fastq preparation</description> | 2 <description>Fastq preparation</description> |
3 <command interpreter="perl"> | 3 <command interpreter="perl"> |
4 PrepareFastqLight.pl -read1_file $input_read1_file -read2_file $input_read2_file -output1 $output_read1_file -output2 $output_read2_file -log_file $log_file -type $quality_type -min_quality $min_quality -min_length $min_length | 4 PrepareFastqLight.pl -read1_file $input_read1_file -read2_file $input_read2_file -output1 $output_read1_file -output2 $output_read2_file -log_file $log_file -type $quality_type -min_quality $min_quality -min_length $min_length |
5 </command> | 5 </command> |
6 <inputs> | 6 <inputs> |
7 <param name="input_read1_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 1 file from your history"/> | 7 <param name="input_read1_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 1 file from your history"/> |
8 <param name="input_read2_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 2 file from your history"/> | 8 <param name="input_read2_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 2 file from your history"/> |
9 <param name="quality_type" type="select" label="Select input quality format"> | 9 <param name="quality_type" type="select" label="Select input quality format"> |
10 <option value="auto" selected="true">Auto-detect</option> | |
10 <option value="sanger">Sanger</option> | 11 <option value="sanger">Sanger</option> |
11 <option value="illumina">Illumina 1.3-1.7</option> | 12 <option value="illumina">Illumina 1.3-1.7</option> |
12 </param> | 13 </param> |
13 <param name="min_quality" type="integer" value="30" label="Minimum quality for 5' and 3' trimming "/> | 14 <param name="min_quality" type="integer" value="30" label="Minimum quality for 5' and 3' trimming "/> |
14 <param name="min_length" type="integer" value="30" label="Minimum sequence length after trimming"/> | 15 <param name="min_length" type="integer" value="30" label="Minimum sequence length after trimming"/> |