Mercurial > repos > nilesh > rseqc
diff infer_experiment.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/infer_experiment.xml Wed Oct 02 02:20:04 2013 -0400 +++ b/infer_experiment.xml Mon Oct 07 15:01:13 2013 -0400 @@ -1,35 +1,35 @@ -<tool id="infer_experiment" name="Infer Experiment" version="1.1"> - <description>speculates how RNA-seq were configured</description> - <requirements> - <requirement type="package" version="1.7.1">numpy</requirement> - <requirement type="package" version="2.3.7">rseqc</requirement> - </requirements> - <command> infer_experiment.py -i $input -r $refgene - - #if $sample_size.boolean - -s $sample_size.size - #end if - - > $output - </command> - <inputs> - <param name="input" type="data" format="bam,sam" label="Input BAM/SAM file" /> - <param name="refgene" type="data" format="bed" label="Reference gene model in bed format" /> - <conditional name="sample_size"> - <param name="boolean" type="boolean" label="Modify usable sampled reads" value="false" /> - <when value="true"> - <param name="size" type="integer" label="Number of usable sampled reads (default = 200000)" value="200000" /> - </when> - </conditional> - </inputs> - <outputs> - <data format="txt" name="output" /> - </outputs> +<tool id="rseqc_infer_experiment" name="Infer Experiment" version="1.1"> + <description>speculates how RNA-seq were configured</description> + <requirements> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="2.3.7">rseqc</requirement> + </requirements> + <command> + infer_experiment.py -i $input -r $refgene + #if $sample_size.boolean + -s $sample_size.size + #end if + + > $output + </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="refgene" type="data" format="bed" label="Reference gene model in bed format" /> + <conditional name="sample_size"> + <param name="boolean" type="boolean" label="Modify usable sampled reads" value="false" /> + <when value="true"> + <param name="size" type="integer" label="Number of usable sampled reads (default = 200000)" value="200000" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="output" /> + </outputs> + <help> infer_experiment.py +++++++++++++++++++ @@ -42,13 +42,13 @@ ++++++++++++++ Input BAM/SAM file - Alignment file in BAM/SAM format. + Alignment file in BAM/SAM format. Reference gene model - Gene model in BED format. + Gene model in BED format. Number of usable sampled reads (default=200000) - Number of usable reads sampled from SAM/BAM file. More reads will give more accurate estimation, but make program little slower. + Number of usable reads sampled from SAM/BAM file. More reads will give more accurate estimation, but make program little slower. Outputs +++++++ @@ -88,37 +88,37 @@ **Example1** :: - ========================================================= - This is PairEnd Data :: + ========================================================= + This is PairEnd Data :: - Fraction of reads explained by "1++,1--,2+-,2-+": 0.4992 - Fraction of reads explained by "1+-,1-+,2++,2--": 0.5008 - Fraction of reads explained by other combinations: 0.0000 - ========================================================= + Fraction of reads explained by "1++,1--,2+-,2-+": 0.4992 + Fraction of reads explained by "1+-,1-+,2++,2--": 0.5008 + Fraction of reads explained by other combinations: 0.0000 + ========================================================= *Conclusion*: We can infer that this is NOT a strand specific because 50% of reads can be explained by "1++,1--,2+-,2-+", while the other 50% can be explained by "1+-,1-+,2++,2--". **Example2** :: - ============================================================ - This is PairEnd Data + ============================================================ + This is PairEnd Data - Fraction of reads explained by "1++,1--,2+-,2-+": 0.9644 :: - Fraction of reads explained by "1+-,1-+,2++,2--": 0.0356 - Fraction of reads explained by other combinations: 0.0000 - ============================================================ - + Fraction of reads explained by "1++,1--,2+-,2-+": 0.9644 :: + Fraction of reads explained by "1+-,1-+,2++,2--": 0.0356 + Fraction of reads explained by other combinations: 0.0000 + ============================================================ + *Conclusion*: We can infer that this is a strand-specific RNA-seq data. strandness of read1 is consistent with that of gene model, while strandness of read2 is opposite to the strand of reference gene model. **Example3** :: - ========================================================= - This is SingleEnd Data :: + ========================================================= + This is SingleEnd Data :: - Fraction of reads explained by "++,--": 0.9840 :: - Fraction of reads explained by "+-,-+": 0.0160 - Fraction of reads explained by other combinations: 0.0000 - ========================================================= + Fraction of reads explained by "++,--": 0.9840 :: + Fraction of reads explained by "+-,-+": 0.0160 + Fraction of reads explained by other combinations: 0.0000 + ========================================================= *Conclusion*: This is single-end, strand specific RNA-seq data. Strandness of reads are concordant with strandness of reference gene. @@ -137,5 +137,5 @@ .. _RSeQC: http://rseqc.sourceforge.net/ - </help> + </help> </tool>