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+++ b/hhsearch.xml	Fri Jul 31 23:16:55 2020 -0400
@@ -0,0 +1,66 @@
+<tool id="hhsearch" name="HHsearch" version="0.1.0" python_template_version="3.5">
+    <description>detecting remote homologues from proteins</description>
+    <requirements>
+        <requirement type="package" version="3.2.0">hhsuite</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        link '$hhm_ffdata' hhdb_hhm.ffdata &&
+        link '$hhm_ffindex' hhdb_hhm.ffindex &&
+        link '$cs219_ffdata' hhdb_cs219.ffdata &&
+        link '$cs219_ffindex' hhdb_cs219.ffindex &&
+        $method -e '$e' -i '$input' -d hhdb -o '$output'
+    ]]></command>
+    <inputs>
+        <param format="data" name="input" type="data" label="Query Sequence" help="Single sequence or multiple sequence alignment (MSA)
+                in a3m, a2m, or FASTA format, or HMM in hhm format. (-i)"/>
+        <param format="txt" name="hhm_ffindex" type="data" label="HHM Index file" help="Database file ending with 'hhm.ffindex'."/>
+        <param format="data" name="hhm_ffdata" type="data" label="HHM Data file" help="Database file ending with 'hhm.ffdata'."/>
+        <param format="txt" name="cs219_ffindex" type="data" label="cs219 Index file" help="Database file ending with 'cs219.ffindex'."/>
+        <param format="data" name="cs219_ffdata" type="data" label="cs219 Data file" help="Database file ending with 'cs219.ffdata'."/>
+        <param name="method" type="select" display="radio" label="Search Method" help="Select a search method. See help below for more information.">
+            <option value="hhsearch" selected="true">HHsearch</option>
+            <option value="hhblits">HHblits</option>
+        </param>
+        <param name="e" type="float" label="E-value cutoff for inclusion in result alignment. (-e)" value="0.001" min="0" max="1"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="method" value="hhblits"/>
+            <param name="input" value="6VYB_A.fasta"/>
+            <param name="hhm_ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffindex"/>
+            <param name="hhm_ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffdata"/>
+            <param name="cs219_ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffindex"/>
+            <param name="cs219_ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffdata"/>
+            <output name="output" file="6VYB_A.hhr" lines_diff="4"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+HHsearch aligns a profile HMM against a database of target profile HMMs. The search first aligns the
+query HMM with each of the target HMMs using the Viterbi dynamic programming algorithm, which finds the
+alignment with the maximum score. The E-value for the target HMM is calculated from the Viterbi score. 
+Target HMMs that reach sufficient significance to be reported are realigned using the Maximum Accuracy algorithm (MAC).
+This algorithm maximizes the expected number of correctly aligned pairs of residues minus a penalty between 0 and 1.
+Values near 0 produce greedy, long, nearly global alignments, values above 0.3 result in shorter, local alignments.
+
+HHblits is an accelerated version of HHsearch that is fast enough to perform iterative searches through millions of profile HMMs,
+e.g. through the Uniclust profile HMM databases, generated by clustering the UniProt database into clusters of globally alignable sequences. 
+Analogously to PSI-BLAST and HMMER3, such iterative searches can be used to build MSAs by starting from a single query sequence.
+Sequences from matches to profile HMMs below some E-value threshold (e.g. 10−3) are added to the query MSA for the next search iteration.
+
+Download databases from: http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubhh-suite,
+  author = {Soeding, Johannes},
+  year = {2005},
+  title = {Protein homology detection by HMM-HMM comparison},
+  publisher = {Oxford University Press},
+  journal = {Bioinformatics},
+  url = {https://doi.org/10.1093/bioinformatics/bti125},
+}</citation>
+    </citations>
+</tool>
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