| Previous changeset 62:8c42a6d7ffd4 (2015-10-19) Next changeset 64:783e6ed4eb66 (2015-10-19) |
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Commit message:
Added a simple test for Clusterize |
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modified:
SMART/galaxy/Clusterize.xml test-data/smart_1.bed |
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added:
.hgignore SMART/galaxy/.Clusterize.xml.swp test-data/smart_clusterize_out_1.gff3 |
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| diff -r 8c42a6d7ffd4 -r 5f210bc9f486 .hgignore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.hgignore Mon Oct 19 12:02:29 2015 +0200 |
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| @@ -0,0 +1,2 @@ +syntax: glob +.*.swp |
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| diff -r 8c42a6d7ffd4 -r 5f210bc9f486 SMART/galaxy/.Clusterize.xml.swp |
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| Binary file SMART/galaxy/.Clusterize.xml.swp has changed |
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| diff -r 8c42a6d7ffd4 -r 5f210bc9f486 SMART/galaxy/Clusterize.xml --- 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 |
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| @@ -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. |
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| diff -r 8c42a6d7ffd4 -r 5f210bc9f486 test-data/smart_1.bed --- a/test-data/smart_1.bed Mon Oct 19 11:25:11 2015 +0200 +++ b/test-data/smart_1.bed Mon Oct 19 12:02:29 2015 +0200 |
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| @@ -1,2 +1,2 @@ -chr1 1000 5000 test1 1000 + -chr1 2000 6000 test2 1000 - +chr1 1000 5000 test1 +chr1 2000 6000 test2 |
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| diff -r 8c42a6d7ffd4 -r 5f210bc9f486 test-data/smart_clusterize_out_1.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/smart_clusterize_out_1.gff3 Mon Oct 19 12:02:29 2015 +0200 |
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| @@ -0,0 +1,1 @@ +chr1 S-MART transcript 1000 5999 . + . nbElements=2.000000;ID=test2--test1;Name=test2--test1 |