Mercurial > repos > fangly > grinder
changeset 2:27a15723d4f0
Uploaded
| author | fangly |
|---|---|
| date | Tue, 04 Oct 2011 01:02:12 -0400 |
| parents | 7d26d64539b2 |
| children | 4812050c5bf9 |
| files | Galaxy_readme.txt tools/ngs_simulation/grinder.xml tools/ngs_simulation/grinder_multiple_outputs.py |
| diffstat | 3 files changed, 23 insertions(+), 10 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy_readme.txt Tue Oct 04 01:02:12 2011 -0400 @@ -0,0 +1,5 @@ +An XML wrapper that provides a GUI for Grinder in Galaxy (http://galaxy.psu.edu/) + +Place these files in your Galaxy directory. More information at http://wiki.g2.bx.psu.edu/FrontPage. + +Note: The Grinder wrapper uses Galaxy buitin datasets located in the 'all_fasta' data table.
--- a/tools/ngs_simulation/grinder.xml Mon Sep 19 01:07:28 2011 -0400 +++ b/tools/ngs_simulation/grinder.xml Tue Oct 04 01:02:12 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="grinder" name="Grinder" version="0.3.7" force_history_refresh="True"> +<tool id="grinder" name="Grinder" version="0.3.8" force_history_refresh="True"> <!-- Author: florent.angly@gmail.com @@ -9,7 +9,7 @@ • Better sync with Grinder parameters, defaults and help --> - <description>genomic, metagenomic and amplicon read simulator (BETA)</description> + <description>genomic, metagenomic and amplicon read simulator</description> <requirements> <requirement type="binary">grinder</requirement> @@ -101,6 +101,9 @@ #if str($qual_levels): -qual_levels $qual_levels #end if + #if str($fastq_output): + -fastq_output $fastq_output + #end if #if str($profile_file) != "None": -profile_file $profile_file.value #end if @@ -215,6 +218,10 @@ <param name="qual_levels" type="text" optional="true" label="Quality score levels" help="Generate basic quality scores for the simulated reads. Good residues are given a specified good score (e.g. 30) and residues that are the result of an insertion or substitution are given a specified bad score (e.g. 10). Specify first the good score and then the bad score, e.g. '30 10'" /> + <param name="fastq_output" type="boolean" truevalue="1" falsevalue="0" checked="false" label="FASTQ output" help=" +Write the generated reads in FASTQ format (Sanger variant) instead of FASTA and +QUAL. Quality score levels need to be specified for this option to be effective." /> + <param name="profile_file" type="data" format="txt" optional="true" label="Profile file" help="A file that contains Grinder arguments. This is useful if you use many options or often use the same options. Lines with comments (#) are ignored. Consider the profile file, 'simple_profile.txt': # A simple Grinder profile
--- a/tools/ngs_simulation/grinder_multiple_outputs.py Mon Sep 19 01:07:28 2011 -0400 +++ b/tools/ngs_simulation/grinder_multiple_outputs.py Tue Oct 04 01:02:12 2011 -0400 @@ -50,6 +50,10 @@ # Assign the dataset format if extension == '.txt': format = 'text' + elif extension == '.fq': + format = 'fastqsanger' + elif extension == '.fastq': + format = 'fastqsanger' elif extension == '.fa': format = 'fasta' elif extension == '.fna': @@ -58,10 +62,6 @@ format = 'fasta' elif extension == '.fasta': format = 'fasta' - elif extension == '.fq': - format = 'fastq' - elif extension == '.fastq': - format = 'fastq' elif extension == '.qual': format = 'qual' else: @@ -72,7 +72,7 @@ match = q.search(basename) if match != None: lib_num = match.group(1) - name = 'lib%s' % lib_num + name = 'lib%s-' % lib_num match = r.search(basename) if match == None: @@ -82,11 +82,12 @@ if format == 'qual': lib_type = 'qual' - name = name + '-' + lib_type + name = name + lib_type # Move the dataset to the proper place - optional_spec = 'asdf' - destination = os.path.join( output_dir, 'primary_%s_%s_visible_%s_%s' % ( output_id, name, format, optional_spec ) ) + #db_ref = '' + #destination = os.path.join( output_dir, 'primary_%s_%s_visible_%s_%s' % (output_id, name, format, db_ref) ) + destination = os.path.join( output_dir, 'primary_%s_%s_visible_%s' % (output_id, name, format) ) print "moving %s to %s" % (source, destination)