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comparison rgFastQC.xml @ 13:9337dd1fbc66 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 8991687e2ec5f75d3841c613ea5d8ffda0389654
author iuc
date Mon, 05 Jun 2017 13:49:57 -0400
parents 484e86282f4b
children 2b0c9d9fc6ca
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12:484e86282f4b 13:9337dd1fbc66
1 <tool id="fastqc" name="FastQC" version="0.68"> 1 <tool id="fastqc" name="FastQC" version="0.69">
2 <description>Read Quality reports</description> 2 <description>Read Quality reports</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.11.5">fastqc</requirement> 4 <requirement type="package" version="0.11.5">fastqc</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <command detect_errors="exit_code"><![CDATA[
7 <exit_code range="1:" /> 7 #import re
8 <exit_code range=":-1" /> 8 #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier))
9 <regex match="Error:" /> 9 python '$__tool_directory__/rgFastQC.py'
10 <regex match="Exception:" />
11 </stdio>
12 <command><![CDATA[
13 python '${__tool_directory__}/rgFastQC.py'
14 -i '$input_file' 10 -i '$input_file'
15 -d '${html_file.files_path}' 11 -d '$html_file.files_path'
16 -o '$html_file' 12 -o '$html_file'
17 -t '$text_file' 13 -t '$text_file'
18 -f '${input_file.ext}' 14 -f '$input_file.ext'
19 -j '${input_file.name}' 15 -j '$input_name'
20 #if $contaminants.dataset and str($contaminants) > '' 16 #if $contaminants.dataset and str($contaminants) > ''
21 -c '$contaminants' 17 -c '$contaminants'
22 #end if 18 #end if
23 #if $limits.dataset and str($limits) > '' 19 #if $limits.dataset and str($limits) > ''
24 -l '$limits' 20 -l '$limits'