--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/malt_index_builder.xml	Tue Oct 12 14:15:35 2021 +0000
@@ -0,0 +1,95 @@
+<tool id="data_manager_malt_index_builder" name="MALT index builder" tool_type="manage_data" version="0.5.3+galaxy0" profile="21.01">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="0.53">malt</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/malt_index_builder.py'
+'${out_file}'
+--fasta_filename '${all_fasta_source.fields.path}'
+--fasta_dbkey '${all_fasta_source.fields.dbkey}'
+--fasta_description '${all_fasta_source.fields.name}'
+--sequence_type '${sequence_type}'
+#if str($seed_setting_cond.seed_setting) == 'yes':
+    --shapes '${seed_setting_cond.shapes}'
+    --max_hits_per_seed $seed_setting_cond.max_hits_per_seed
+    --protein_reduct '${seed_setting_cond.protein_reduct}'
+#end if
+    ]]></command>
+    <inputs>
+        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
+            <options from_data_table="all_fasta"/>
+        </param>
+        <param name="sequence_name" type="text" value="" label="Name of sequence" />
+        <param name="sequence_id" type="text" value="" label="ID for sequence" />
+        <param  name="sequence_type" type="select" label="Specify whether the reference sequences are DNA or Protein sequences" help="Use the DNA setting For RNA sequences">
+            <option value="DNA" selected="true">DNA</option>
+            <option value="Protein">Protein</option>
+        </param>
+        <conditional name="seed_setting_cond">
+            <param name="seed_setting" type="select" label="Specify seed settings?">
+                <option selected="true" value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param name="shapes" type="text" value="" label="Comma-separated list of seed shapes" help="See help text below">
+                    <sanitizer invalid_char="">
+                        <valid initial="string.printable">
+                            <remove value="&apos;" />
+                        </valid>
+                        <mapping initial="none">
+                            <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
+                        </mapping>
+                    </sanitizer>
+                </param>
+                <param name="max_hits_per_seed" type="integer" value="1" min="1" label="Maximum number of hits per seed"/>
+                <param name="protein_reduct" type="select" label="Name or definition of protein alphabet reduction">
+                    <option selected="true" value="DIAMOND_11">DIAMOND_11</option>
+                    <option value="BLOSUM50_10">BLOSUM50_10</option>
+                    <option value="BLOSUM50_11">BLOSUM50_11</option>
+                    <option value="BLOSUM50_15">BLOSUM50_15</option>
+                    <option value="BLOSUM50_4">BLOSUM50_4</option>
+                    <option value="BLOSUM50_8">BLOSUM50_8</option>
+                    <option value="GBMR4">GBMR4</option>
+                    <option value="HSDM17">HSDM17</option>
+                    <option value="MALT_10">MALT_10</option>
+                    <option value="SDM12">SDM12</option>
+                    <option value="UNREDUCED">UNREDUCED</option>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="all_fasta_source" value="phiX174"/>
+            <output name="out_file" value="malt_index_builder.json"/>
+        </test>
+    </tests>
+    <help>
+.. class:: infomark
+
+**Notice:** Values for name, description, and id will be generated automatically if left blank.
+
+**What it does**
+
+Takes a reference sequence database (represented by a FastA file, possibly in gzip format) as input and produces an index that
+can be used by the malt tool as input. If MALT is to be used as a taxonomic and/or functional analysis tool as well as an
+alignment tool, then this MALT index builder tool must be provided with a number of mapping files that are used to map reference
+sequences to taxonomic or functional classes or to locate genes in DNA reference sequences.
+
+**Options**
+
+ * **Specify seed settings** - specify the settings for controlling how MALT uses its seed-and-extend approach based on “spaced seeds”.
+
+  * **Shapes** - specify the seed shapes used. For DNA sequences, the default seed shape is: 111110111011110110111111. For protein sequences, by default MALT uses the following four shapes: 111101101110111, 1111000101011001111, 11101001001000100101111 and 11101001000010100010100111.
+  * **Maximim hits per seed** - specify the maximum number of hits per seed - MALT uses this to calculate a maximum number of hits per hash value.
+  * **Protein reduction** - specify the alphabet reduction in the case of protein reference sequences. By default, MALT reduces amino acids to 8 different letters, grouped as follows: [LVIMC] [AG] [ST] [P] [FYW] [EDNQ] [KR] [H].
+    </help>
+    <citations>
+        <citation type="doi">https://doi.org/10.1101/050559</citation>
+    </citations>
+</tool>