Mercurial > repos > devteam > fastqc

comparison rgFastQC.xml @ 14:da652f6f84cc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 9a987a679243f52297c465180da0bb557a3d0fa7
author iuc
date Sun, 14 Jan 2018 09:31:33 -0500
parents 7d8c56e1a3aa
children d44f3c8ed647
comparison
equal deleted inserted replaced
13:7d8c56e1a3aa 14:da652f6f84cc
1 <tool id="fastqc" name="FastQC" version="0.70"> 1 <tool id="fastqc" name="FastQC" version="0.71">
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="0.11.6">fastqc</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 #import re 7 #import re
8 #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier)) 8 #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier))
9 9
20 #elif 'sam' in $input_file.ext: 20 #elif 'sam' in $input_file.ext:
21 #set format = 'sam' 21 #set format = 'sam'
22 #else 22 #else
23 #set format = 'fastq' 23 #set format = 'fastq'
24 #end if 24 #end if
25
26 25
27 ln -s '${input_file}' '${input_file_sl}' && 26 ln -s '${input_file}' '${input_file_sl}' &&
28 mkdir -p '${html_file.files_path}' && 27 mkdir -p '${html_file.files_path}' &&
29 fastqc 28 fastqc
30 --outdir '${html_file.files_path}' 29 --outdir '${html_file.files_path}'
61 <tests> 60 <tests>
62 <test> 61 <test>
63 <param name="input_file" value="1000gsample.fastq" /> 62 <param name="input_file" value="1000gsample.fastq" />
64 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" /> 63 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
65 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/> 64 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
66 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/> 65 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="4"/>
67 </test> 66 </test>
68 <test> 67 <test>
69 <param name="input_file" value="1000gsample.fastq" /> 68 <param name="input_file" value="1000gsample.fastq" />
70 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" /> 69 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
71 <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/> 70 <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/>
72 <output name="text_file" file="fastqc_data2.txt" ftype="txt" lines_diff="2"/> 71 <output name="text_file" file="fastqc_data2.txt" ftype="txt" lines_diff="4"/>
73 </test> 72 </test>
74 <test> 73 <test>
75 <param name="input_file" value="1000gsample.fastq.gz" ftype="fastq.gz" /> 74 <param name="input_file" value="1000gsample.fastq.gz" ftype="fastq.gz" />
76 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" /> 75 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
77 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/> 76 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
78 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/> 77 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="4"/>
79 </test> 78 </test>
80 <test> 79 <test>
81 <param name="input_file" value="1000gsample.fastq.bz2" ftype="fastq.bz2" /> 80 <param name="input_file" value="1000gsample.fastq.bz2" ftype="fastq.bz2" />
82 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" /> 81 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
83 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/> 82 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
84 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/> 83 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="4"/>
85 </test> 84 </test>
86 <test> 85 <test>
87 <param name="input_file" value="hisat_output_1.bam" ftype="bam" /> 86 <param name="input_file" value="hisat_output_1.bam" ftype="bam" />
88 <output name="html_file" file="fastqc_report_hisat.html" ftype="html" lines_diff="100"/> 87 <output name="html_file" file="fastqc_report_hisat.html" ftype="html" lines_diff="100"/>
89 <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt" lines_diff="2"/> 88 <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt" lines_diff="4"/>
90 </test> 89 </test>
91 </tests> 90 </tests>
92 <help> 91 <help>
93 .. class:: infomark 92 .. class:: infomark
94 93