Mercurial > repos > devteam > fastqc
changeset 9:3a458e268066 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e
| author | devteam |
|---|---|
| date | Wed, 02 Nov 2016 16:12:51 -0400 |
| parents | 06819360a9e2 |
| children | a00a6402d09a |
| files | rgFastQC.py rgFastQC.xml test-data/1000gsample.fastq.gz |
| diffstat | 3 files changed, 16 insertions(+), 5 deletions(-) [+] |
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--- a/rgFastQC.py Mon Oct 31 10:40:12 2016 -0400 +++ b/rgFastQC.py Wed Nov 02 16:12:51 2016 -0400 @@ -28,6 +28,7 @@ import gzip import bz2 import zipfile +import mimetypes class FastQCRunner(object): @@ -52,7 +53,8 @@ trimext = False # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf # patched may 29 2013 until this is fixed properly - if ( linf.endswith('.gz') or linf.endswith('.gzip') ): + type = mimetypes.guess_type(self.opts.input) + if linf.endswith('.gz') or linf.endswith('.gzip') or type[-1] == "gzip": f = gzip.open(self.opts.input) try: f.readline() @@ -95,8 +97,11 @@ command_line.append('--limits %s' % opts.limits) command_line.append('--quiet') command_line.append('--extract') # to access the output text file + if type[-1] != "gzip": + command_line.append('-f %s' % opts.informat) + else: + self.fastqinfilename += ".gz" command_line.append(self.fastqinfilename) - command_line.append('-f %s' % opts.informat) self.command_line = ' '.join(command_line) def copy_output_file_to_dataset(self):
--- a/rgFastQC.xml Mon Oct 31 10:40:12 2016 -0400 +++ b/rgFastQC.xml Wed Nov 02 16:12:51 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="fastqc" name="FastQC" version="0.66"> +<tool id="fastqc" name="FastQC" version="0.67"> <description>Read Quality reports</description> <requirements> <requirement type="package" version="0.11.5">fastqc</requirement> @@ -48,6 +48,12 @@ <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/> <output name="text_file" file="fastqc_data2.txt" ftype="txt" compare="sim_size"/> </test> + <test> + <param name="input_file" value="1000gsample.fastq.gz" /> + <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" /> + <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/> + <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/> + </test> </tests> <help> @@ -63,7 +69,7 @@ The main functions of FastQC are: -- Import of data from BAM, SAM or FastQ files (any variant) +- Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant), - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report @@ -94,7 +100,7 @@ FastQC_ is the best place to look for documentation - it's very good. A summary follows below for those in a tearing hurry. -This wrapper will accept a Galaxy fastq, sam or bam as the input read file to check. +This wrapper will accept a Galaxy fastq, fastq.gz, sam or bam as the input read file to check. It will also take an optional file containing a list of contaminants information, in the form of a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom limits.txt file that allows setting the warning thresholds for the different modules and also specifies