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comparison rapsodyn/PrepareFastqLight.xml @ 7:3f7b0788a1c4 draft

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author mcharles
date Tue, 07 Oct 2014 10:34:34 -0400
parents 442a7c88b886
children d857538d9fea
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6:1776b8ddd87e 7:3f7b0788a1c4
1 <tool id="PrepareFastqLight" name="PrepareFastqLight" version="0.01"> 1 <tool id="PrepareFastqLight" name="PrepareFastqLight" version="1.01">
2 <description>Fastq preparation</description> 2 <description>Fastq preparation</description>
3 <command interpreter="perl"> 3 <command interpreter="perl">
4 PrepareFastqLight.pl $input_read1_file $input_read2_file $output_read1_file $output_read2_file $quality_type $min_quality $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 $min_length
5 </command> 5 </command>
6 <inputs> 6 <inputs>
7 <param name="input_read1_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 1 file from your history"/> 7 <param name="input_read1_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 1 file from your history"/>
8 <param name="input_read2_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 2 file from your history"/> 8 <param name="input_read2_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 2 file from your history"/>
9 <param name="quality_type" type="select" label="Select input quality format"> 9 <param name="quality_type" type="select" label="Select input quality format">
10 <option value="sanger">Sanger</option> 10 <option value="sanger">Sanger</option>
11 <option value="illumina">Illumina 1.3-1.7</option> 11 <option value="illumina">Illumina 1.3-1.7</option>
12 </param> 12 </param>
13 <param name="min_quality" type="integer" value="30" label="Minimum quality for 5' and 3' trimming "/> 13 <param name="min_quality" type="integer" value="30" label="Minimum quality for 5' and 3' trimming "/>
14 <param name="min_length" type="integer" value="30" label="Minimum sequence length after trimming"/> 14 <param name="min_length" type="integer" value="30" label="Minimum sequence length after trimming"/>
15 </inputs> 15 </inputs>
16 <outputs> 16 <outputs>
17 <data name="output_read1_file" format="fastqsanger" label="${tool.name} on ${on_string}"/> 17 <data name="output_read1_file" format="fastqsanger" label="${tool.name} on ${on_string}"/>
18 <data name="output_read2_file" format="fastqsanger" label="${tool.name} on ${on_string}"/> 18 <data name="output_read2_file" format="fastqsanger" label="${tool.name} on ${on_string}"/>
19 <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
19 </outputs> 20 </outputs>
20 21
21 <help> 22 <help>
22 23
23 24