Mercurial > repos > bgruening > trim_galore
changeset 2:9109c2c3be1e draft
Uploaded
author | bgruening |
---|---|
date | Fri, 19 Jul 2013 09:37:45 -0400 |
parents | 898db63d2e84 |
children | eb546ac2aab2 |
files | tool_dependencies.xml trim_galore_wrapper.xml |
diffstat | 2 files changed, 2 insertions(+), 23 deletions(-) [+] |
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--- a/tool_dependencies.xml Wed Jul 17 15:05:43 2013 -0400 +++ b/tool_dependencies.xml Fri Jul 19 09:37:45 2013 -0400 @@ -20,23 +20,6 @@ <readme> </readme> </package> - <package name="fastqc" version="0.10.1"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip</action> - <action type="move_directory_files"> - <source_directory>../FastQC/</source_directory> - <destination_directory>$INSTALL_DIR/FastQC</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/FastQC</environment_variable> - </action> - </actions> - </install> - <readme> - FastQC needs a java Runtime Environment. - </readme> - </package> </tool_dependency>
--- a/trim_galore_wrapper.xml Wed Jul 17 15:05:43 2013 -0400 +++ b/trim_galore_wrapper.xml Fri Jul 19 09:37:45 2013 -0400 @@ -4,7 +4,6 @@ <version_command interpreter="perl">trim_galore --version</version_command> <requirements> <requirement type="package" version="1.1">cutadapt</requirement> - <requirement type="package" version="0.10.1">fastqc</requirement> </requirements> <command interpreter="perl"> #from glob import glob @@ -49,7 +48,6 @@ #if $params.settingsType == "custom": - $params.fastqc ## default 20 --quality $params.quality ## default 'AGATCGGAAGAGC' @@ -178,7 +176,7 @@ #end if ## delete the temp_dir - ##rm -rf $temp_dir + rm -rf $temp_dir </command> <inputs> @@ -211,7 +209,6 @@ <when value="default" /> <!-- Full/advanced params. --> <when value="custom"> - <param name="fastqc" type="boolean" truevalue="--fastqc" falsevalue="" checked="False" label="Run FastQC in the default mode on the FastQ file once trimming is complete" help="" /> <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal." help="For more information please see below." /> <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed"> <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator> @@ -330,8 +327,7 @@ **What it does** TrimGalore!_ is a wrapper script that makes use of the publically available -adapter trimming tool Cutadapt and FastQC for optional quality control once -the trimming process has completed. +adapter trimming tool Cutadapt. .. _TrimGalore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/