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comparison FastQC/rgFastQC.xml @ 9:c13fa2748191 draft

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author fubar
date Mon, 03 Jun 2013 23:25:42 -0400
parents 42251cbdeeac
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8:c5afa527c8b8 9:c13fa2748191
1 <tool name="FastQC: Comprehensive QC" id="fastqc" version="0.53"> 1 <tool name="FastQC: Comprehensive QC" id="fastqc" version="0.53">
2 <description>reporting for short read sequence</description> 2 <description>reporting for short read sequence</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "\$FASTQC_INSTALL_PATH/fastqc" 4 rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "\$FASTQC_BINARY_PATH"
5 #if $contaminants.dataset and str($contaminants) > '' 5 #if $contaminants.dataset and str($contaminants) > ''
6 -c "$contaminants" 6 -c "$contaminants"
7 #end if 7 #end if
8 </command> 8 </command>
9 <requirements> 9 <requirements>
10 <requirement type="set_environment">FASTQC_INSTALL_PATH</requirement> 10 <requirement type="set_environment">FASTQC_BINARY_PATH</requirement>
11 <requirement type="package" version="0.10.1">FastQC</requirement> 11 <requirement type="package" version="0.10.1">FastQC</requirement>
12 </requirements> 12 </requirements>
13 <inputs> 13 <inputs>
14 <param format="fastqsanger,fastq,bam,sam" name="input_file" type="data" label="Short read data from your current history" /> 14 <param format="fastqsanger,fastq,bam,sam" name="input_file" type="data" label="Short read data from your current history" />
15 <param name="out_prefix" value="FastQC" type="text" label="Title for the output file - to remind you what the job was for" size="80" 15 <param name="out_prefix" value="FastQC" type="text" label="Title for the output file - to remind you what the job was for" size="80"