# HG changeset patch
# User bitlab
# Date 1545067499 18000
# Node ID fc3f2aefe244a9a3f907f1a9143f014387e9ce61
# Parent  4616cc3476d4eda5b7e8f6dd298608022480ee0d
Uploaded

diff -r 4616cc3476d4 -r fc3f2aefe244 chromeister/chromeister.xml
--- a/chromeister/chromeister.xml	Sat Dec 15 18:06:48 2018 -0500
+++ b/chromeister/chromeister.xml	Mon Dec 17 12:24:59 2018 -0500
@@ -1,14 +1,31 @@
-<tool id="chromeister" name="Chromeister">
-   <description>A heuristic approach for ultra fast previsualization of pairwise genome comparisons</description>
-   <inputs>
-      <param name="query" type="data" format="fasta" label="Query sequence" help="Query sequence file in fasta format" />
-      <param name="db" type="data" format="fasta" label="Reference sequence" help="Reference sequence file in fasta format" />
-      <param name="dimension" type="integer" value="1000" label="Dimension" help="Compression size" />
-   </inputs>
-   <command>echo "\$PWD"; cp $query ${query.name}; cp $db ${db.name}; (/home/galaxy-bitlab/galaxy/tools/chromeister/bin/CHROMEISTER -query ${query.name} -db ${db.name} -dimension $dimension -out ${query.name}-${db.name}.mat) &amp;>/dev/null ; rm ${query.name}; rm ${db.name}; Rscript /home/galaxy-bitlab/galaxy/tools/chromeister/bin/compute_score.R  ${query.name}-${db.name}.mat $dimension; mv ${query.name}-${db.name}.mat $output; mv ${query.name}-${db.name}.mat.filt.png $outputIMAGEN ; mv ${query.name}-${db.name}.mat.events.txt $outputEVENTS; rm hits-XY-${query.name}-${db.name}.mat.hits</command>
-  <outputs>
-      <data name="output" format="txt" label="Comparison matrix"/>
-      <data name="outputIMAGEN" format="png" label="Comparison dotplot"/>
-      <data name="outputEVENTS" format="txt" label="Detected events"/>
-  </outputs>
-</tool>
+<tool id="chromeister" name="Chromeister">
+   <description>A heuristic approach for ultra fast previsualization of pairwise genome comparisons</description>
+   <inputs>
+      <param name="query" type="data" format="fasta" label="Query sequence" help="Query sequence file in fasta format" />
+      <param name="db" type="data" format="fasta" label="Reference sequence" help="Reference sequence file in fasta format" />
+      <param name="dimension" type="integer" value="1000" label="Dimension" help="Compression size" />
+   </inputs>
+   <command>echo "\$PWD"; cp $query ${query.name}; cp $db ${db.name}; (/home/galaxy-bitlab/galaxy/tools/chromeister/bin/CHROMEISTER -query ${query.name} -db ${db.name} -dimension $dimension -out ${query.name}-${db.name}.mat) &amp;>/dev/null ; rm ${query.name}; rm ${db.name}; Rscript /home/galaxy-bitlab/galaxy/tools/chromeister/bin/compute_score.R  ${query.name}-${db.name}.mat $dimension; mv ${query.name}-${db.name}.mat $output; mv ${query.name}-${db.name}.mat.filt.png $outputIMAGEN ; mv ${query.name}-${db.name}.mat.events.txt $outputEVENTS; rm hits-XY-${query.name}-${db.name}.mat.hits</command>
+  <outputs>
+      <data name="output" format="txt" label="Comparison matrix"/>
+      <data name="outputIMAGEN" format="png" label="Comparison dotplot"/>
+      <data name="outputEVENTS" format="txt" label="Detected events"/>
+  </outputs>
+
+  <help>
+
+Chromeister is a heuristic approach for ultra fast previsualization of pairwise genome comparisons. It is able to compare enormous genomes (up to 30 thousand million base pairs, or 10 times the size of the human genome) much faster than other methods while yielding significant, reusable and exploitable information.
+
+-----
+
+**Manual**
+
+To use Chromeister, simply upload two metagenomes in the fasta format and select these as Query and Reference metagenome. Once so, choose the dimension (compression size) that suit best your comparison.
+
+  </help>
+
+  <citations>
+  </citations>
+
+
+</tool>