# HG changeset patch
# User bitlab
# Date 1545067241 18000
# Node ID 353e5673bcb8c469a7c0ae9bb1870b9a26a74e14
# Parent  7430449b881411471344db841293b96efd93bbb7
Uploaded

diff -r 7430449b8814 -r 353e5673bcb8 IMSAME/IMSAME.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IMSAME/IMSAME.xml	Mon Dec 17 12:20:41 2018 -0500
@@ -0,0 +1,39 @@
+<tool id="IMSAME" name="IMSAME">
+   <description>A Pairwise Incremental Multi-Staged Alignment Method for Metagenomes Comparison</description>
+   <inputs>
+      <param name="query" type="data" format="fasta" label="Query metagenome" help="Query sequence file in fasta format" />
+      <param name="db" type="data" format="fasta" label="Reference metagenome" help="Reference sequence file in fasta format" />
+      <param name="evalue" type="text" size="30" value="10e-10" label="Evalue" help="Evalue for filtering HSPs" />
+      <param name="coverage" type="float" value="0.5" label="Coverage" help="Minimum coverage to accept an alignment" />
+      <param name="identity" type="float" value="0.5" label="Identity" help="Minimum identity to accept an alignment" />
+      <param name="kmer" type="integer" value="12" label="Word size" help="Word size for heuristicly exploring the search space" />
+   </inputs>
+   <command>/home/galaxy-bitlab/galaxy/tools/IMSAME/bin/IMSAME -query $query -db $db -evalue $evalue -coverage $coverage -identity $identity -kmer $kmer -out $output --full</command>
+  <outputs>
+      <data name="output" type="txt" label="Output alignments"/>
+  </outputs>
+
+  <help>
+
+IMSAME (Incremental Multi-Stage Alignment of MEtagenomes) is a highly parallel, fine-grained software for the pairwise alignment of metagenomes specifically designed for accurately finding conserved homology signals across metagenomic sequences.
+
+-----
+
+**Manual**
+
+To use IMSAME, simply upload two metagenomes in the fasta format and select these as Query and Reference metagenome. Once so, choose the parameters that suit best your comparison:
+
+- Evalue: This parameter is the minimum expected value required for an alignment to be reported.
+
+- Coverage: This parameter is the minimum coverage to report an alignment. Coverage is the length of the alignment divided by the length of the query read.
+
+- Identity: This parameter is the minimum identity to report an alignment.
+
+- Word size: This parameter is the seed size used for heuristically exploring the search space.
+
+   </help>
+
+   <citations>
+           <citation type="doi">10.1089/cmb.2018.0081</citation>
+   </citations>
+</tool>
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