Mercurial > repos > fangly > grinder
diff tools/ngs_simulation/grinder.xml @ 2:27a15723d4f0
Uploaded
| author | fangly |
|---|---|
| date | Tue, 04 Oct 2011 01:02:12 -0400 |
| parents | 7d26d64539b2 |
| children |
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--- 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