Mercurial > repos > yufei-luo > s_mart
changeset 63:5f210bc9f486
Added a simple test for Clusterize
| author | m-zytnicki |
|---|---|
| date | Mon, 19 Oct 2015 12:02:29 +0200 |
| parents | 8c42a6d7ffd4 |
| children | 783e6ed4eb66 4ab9c86890ba |
| files | .hgignore SMART/galaxy/.Clusterize.xml.swp SMART/galaxy/Clusterize.xml test-data/smart_1.bed test-data/smart_clusterize_out_1.gff3 |
| diffstat | 5 files changed, 17 insertions(+), 2 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.hgignore Mon Oct 19 12:02:29 2015 +0200 @@ -0,0 +1,2 @@ +syntax: glob +.*.swp
--- a/SMART/galaxy/Clusterize.xml Mon Oct 19 11:25:11 2015 +0200 +++ b/SMART/galaxy/Clusterize.xml Mon Oct 19 12:02:29 2015 +0200 @@ -51,6 +51,18 @@ <data name="outputFileGff" format="gff3"/> </outputs> + <tests> + <test> + <!-- basic test --> + <param name="FormatInputFileName" value="bed"/> + <param name="inputFileName" value="smart_1.bed" ftype="bed"/> + <param name="colinear" value="false"/> + <param name="normalize" value="false"/> + <param name="distance" value="0"/> + <output name="output" file="smart_clusterize_out_1.gff3" ftype="gff3"/> + </test> + </tests> + <help> The script clusterizes the input genomic data. Two features are clusterized when their genomic intervals overlap. The output is a GFF3 file, where each element is a cluster. The number of elements in the cluster is given by the tag **nbElements**. The name of a cluster is the concatation of the names of its reads (like **read1--read2--read3**). Note that if the size of the name of the cluster exceeds 100 characters, it is truncated to the first 100 characters.