Mercurial > repos > nilesh > rseqc
diff read_quality.xml @ 32:580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
| author | lparsons |
|---|---|
| date | Mon, 07 Oct 2013 15:01:13 -0400 |
| parents | cc5eaa9376d8 |
| children |
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--- a/read_quality.xml Wed Oct 02 02:20:04 2013 -0400 +++ b/read_quality.xml Mon Oct 07 15:01:13 2013 -0400 @@ -1,26 +1,27 @@ -<tool id="read_quality" name="Read Quality" version="1.1"> - <description>determines Phred quality score</description> - <requirements> - <requirement type="package" version="2.11.0">R</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - <requirement type="package" version="2.3.7">rseqc</requirement> - </requirements> - <command> read_quality.py -i $input -o output -r $reduce - </command> - <inputs> - <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> - <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" /> - </inputs> - <outputs> - <data format="r" name="outputr" from_work_dir="output.qual.r" label="${tool.name} on ${on_string} (R Script)" /> - <data format="pdf" name="outputpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap PDF)" /> - <data format="pdf" name="outputpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot PDF)" /> - </outputs> +<tool id="rseqc_read_quality" name="Read Quality" version="1.1"> + <description>determines Phred quality score</description> + <requirements> + <requirement type="package" version="3.0.1">R</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="2.3.7">rseqc</requirement> + </requirements> + <command> + read_quality.py -i $input -o output -r $reduce + </command> <stdio> <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> </stdio> - <help> + <inputs> + <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> + <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" /> + </inputs> + <outputs> + <data format="txt" name="outputr" from_work_dir="output.qual.r" label="${tool.name} on ${on_string} (R Script)" /> + <data format="pdf" name="outputpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap PDF)" /> + <data format="pdf" name="outputpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot PDF)" /> + </outputs> + <help> read_quality.py +++++++++++++++ @@ -37,10 +38,10 @@ ++++++++++++++ Input BAM/SAM file - Alignment file in BAM/SAM format. + Alignment file in BAM/SAM format. Ignore phred scores less than this number (default=1000) - To avoid making huge vector in R, nucleotide with certain phred score represented less than this number will be ignored. Increase this number save more memory while reduce precision. This option only applies to the 'boxplot'. + To avoid making huge vector in R, nucleotide with certain phred score represented less than this number will be ignored. Increase this number save more memory while reduce precision. This option only applies to the 'boxplot'. Output ++++++++++++++ @@ -73,5 +74,5 @@ .. _RSeQC: http://rseqc.sourceforge.net/ - </help> + </help> </tool>