--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hhsearch.xml	Tue Mar 23 21:38:01 2021 +0000
@@ -0,0 +1,138 @@
+<tool id="hhsearch" name="HHsearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <description>detecting remote homologues of proteins</description>
+    <macros>
+        <token name="@TOOL_VERSION@">3.2.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <xml name="ffindex_single_inputs">
+            <param name="ffdata" type="data" format="ffdata" label="PDB Database" help="Database Data file." />
+            <param name="ffindex" type="data" format="ffindex" label="PDB Database Index" help="Database Index file." />
+        </xml>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">hhsuite</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $db_source.db_source_selector == 'indexed':
+            ln -s '${db_source.ffindex.fields.path}.ffdata' hhdb_hhm.ffdata &&
+            ln -s '${db_source.ffindex.fields.path}.ffindex' hhdb_hhm.ffindex &&
+        #else
+            ln -s '$db_source.ffdata' hhdb_hhm.ffdata &&
+            ln -s '$db_source.ffindex' hhdb_hhm.ffindex &&
+        #end if
+
+        #if $db_source_cs219.db_source_selector == 'indexed':
+            ln -s '${db_source_cs219.ffindex.fields.path}.ffdata' hhdb_cs219.ffdata &&
+            ln -s '${db_source_cs219.ffindex.fields.path}.ffindex' hhdb_cs219.ffindex &&
+        #else
+            ln -s '$db_source_cs219.ffdata' hhdb_cs219.ffdata &&
+            ln -s '$db_source_cs219.ffindex' hhdb_cs219.ffindex &&
+        #end if
+
+        $method
+        -cpu \${GALAXY_SLOTS:-1}
+        -e '$e'
+        -i '$i'
+        -d hhdb
+        -o '$output'
+    ]]>    </command>
+    <inputs>
+        <param argument="--i" type="data" format="fasta,hmm3" label="Query Sequence" help="Single sequence or multiple sequence alignment (MSA)
+                in FASTA format, or HMM in hhm3 format." />
+        <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>
+        <conditional name="db_source">
+            <param name="db_source_selector" type="select" label="Custom or built-in HHM index" help="Built-ins have been indexed using ffindex">
+                <option value="indexed" selected="true">Use a built-in index</option>
+                <option value="history">Use a HHM index from history</option>
+            </param>
+            <when value="indexed">
+                <param name="ffindex" type="select" label="Select ffindex" help="">
+                    <options from_data_table="ffindex_indices">
+                        <filter type="sort_by" column="0" />
+                        <filter type="static_value" column="3" value="hhm" />
+                        <validator type="no_options" message="No indices are available" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <expand macro="ffindex_single_inputs" />
+            </when>
+        </conditional>
+
+        <conditional name="db_source_cs219">
+            <param name="db_source_selector" type="select" label="Custom or built-in cs219 index" help="Built-ins have been indexed using ffindex">
+                <option value="indexed" selected="true">Use a built-in index</option>
+                <option value="history">Use a cs219 index from history</option>
+            </param>
+            <when value="indexed">
+                <param name="ffindex" type="select" label="Select ffindex" help="">
+                    <options from_data_table="ffindex_indices">
+                        <filter type="sort_by" column="0" />
+                        <filter type="static_value" column="3" value="cs219" />
+                        <validator type="no_options" message="No indices are available" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <expand macro="ffindex_single_inputs" />
+            </when>
+        </conditional>
+        <param name="e" type="float" value="0.001" min="0" max="1" label="E-value cutoff for inclusion in result alignment. (-e)" />
+    </inputs>
+    <outputs>
+        <data format="hhr" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="method" value="hhblits" />
+            <param name="i" value="6VYB_A.fasta" />
+            <conditional name="db_source">
+                <param name="db_source_selector" value="history" />
+                <param name="ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffindex" />
+                <param name="ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffdata" />
+            </conditional>
+            <conditional name="db_source_cs219">
+                <param name="db_source_selector" value="history" />
+                <param name="ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffindex" />
+                <param name="ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffdata" />
+            </conditional>
+            <output name="output" file="6VYB_A.hhr" lines_diff="4" ftype="hhr" />
+        </test>
+        <test>
+            <param name="method" value="hhblits" />
+            <param name="i" value="6VYB_A.fasta" />
+            <conditional name="db_source">
+                <param name="db_source_selector" value="indexed" />
+                <param name="ffindex" value="hmm_dbcan" />
+            </conditional>
+            <conditional name="db_source_cs219">
+                <param name="db_source_selector" value="indexed" />
+                <param name="ffindex" value="cs219_dbcan" />
+            </conditional>
+            <output name="output" file="6VYB_A.hhr" lines_diff="4" ftype="hhr" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+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="doi">10.1093/bioinformatics/bti125</citation>
+    </citations>
+</tool>
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