# HG changeset patch
# User bitlab
# Date 1545067217 18000
# Node ID 7430449b881411471344db841293b96efd93bbb7
# Parent  09d02332c84cf866190e4f34f375cfac2e2eb74a
Deleted selected files

diff -r 09d02332c84c -r 7430449b8814 IMSAME.xml
--- a/IMSAME.xml	Mon Dec 17 12:19:58 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-<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>
\ No newline at end of file