Mercurial > repos > devteam > fastqc
comparison rgFastQC.xml @ 13:9337dd1fbc66 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 8991687e2ec5f75d3841c613ea5d8ffda0389654
author | iuc |
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date | Mon, 05 Jun 2017 13:49:57 -0400 |
parents | 484e86282f4b |
children | 2b0c9d9fc6ca |
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12:484e86282f4b | 13:9337dd1fbc66 |
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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' |