Add deacon and deacon DM

data_managers/data_manager_deacon/.shed.yml

@@ -0,0 +1,10 @@
+categories:
+- Data Managers
+- Metagenomics
+homepage_url: https://github.com/bede/deacon
+description: Data manager for Deacon index files
+long_description: Data manager for Deacon index files
+name: deacon_build_database
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_deacon
+type: unrestricted

data_managers/data_manager_deacon/data_manager/deacon_datamanager.xml

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+<tool id="deacon_build_database" name="Deacon" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>database builder</description>
+    <macros>
+        <!-- on update run a local test setting `test` to something else than "true" -->
+        <token name="@TOOL_VERSION@">0.12.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">26.0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">deacon</requirement>
+        <requirement type="package" version="1.6.1">zenodo_get</requirement>
+        <requirement type="package" version="1.25.0">wget</requirement>
+        <requirement type="package" version="8.21.0">curl</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p '$out_file.extra_files_path' &&
+        #if $test != "true"
+            #if $input.is_select == "prebuilt"
+                #if $download == "human"
+                    zenodo_get 17288185 -m -g "*.idx" -o '$out_file.extra_files_path' &&
+                #else
+                    zenodo_get 17699167 -m -g "*.idx" -o '$out_file.extra_files_path' &&
+                #end if
+            #else
+                deacon index build '$input.from_dm.fields.path' -o '${str($input.from_dm.fields.path).split('/')[-1]}.idx' &&
+                mv '${str($input.from_dm.fields.path).split('/')[-1]}.idx' '$out_file.extra_files_path' &&
+            #end if
+        #else
+            touch '$out_file.extra_files_path'/test.idx &&
+        #end if
+        cp '$dmjson' '$out_file'
+    ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[
+#from datetime import datetime
+#set time=datetime.now().strftime("%Y-%m-%d")
+{
+  "data_tables":{
+    "deacon":[
+      {
+        #if $input.is_select == "prebuilt"
+            #if $download == "human"
+                "path":"panhuman-1.k31w15.idx",
+            #else
+                "path":"panmouse-1.k31w15.idx",
+            #end if,
+        #else
+            "path":"${str($input.from_dm.fields.path).split('/')[-1]}.idx",
+        #end if
+            "dbkey":"",
+        #if $input.is_select == "prebuilt"
+            #if $download == "human"
+                "name":"panhuman-1 (k=31, w=15)",
+            #else
+                "name":"panmouse-1 (k=31, w=15, e=0.5)",
+            #end if
+        #else
+            "name":"${str($input.from_dm.fields.path).split('/')[-1]} (k=31, w=15)",
+        #end if
+        #if $input.is_select == "prebuilt"
+            "version":"@TOOL_VERSION@",
+        #else
+            "version":"@TOOL_VERSION@",
+        #end if
+        #if $input.is_select == "prebuilt"
+            "value":"prebuilt-${time}",
+        #else
+            "value":"custom-${time}",
+        #end if
+        "format_version":"3",
+        #if $input.is_select == "prebuilt"
+            "note":"Prebuilt index files from the devs of deacon"
+        #else
+            "note":"Build from fasta file ${str($input.from_dm.fields.path).split('/')[-1]}"
+        #end if
+      }
+    ]
+  }
+}]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <conditional name="input">
+            <param name="is_select" type="select" label="Choose how to add data to the DM">
+                <option value="prebuilt" selected="true">Download a prebuilt file</option>
+                <option value="fastx">Build index file from downloaded fasta files</option>
+            </param>
+            <when value="prebuilt">
+                <param name="download" type="select" label="Select which prebuilt should be downloaded" help="See help section for more information">
+                    <option value="human">panhuman-1 (k=31, w=15)</option>
+                    <option value="mouse">panmouse-1 (k=31, w=15, e=0.5)</option> 
+                </param>
+            </when>
+            <when value="fastx">
+                <param name="from_dm" type="select" label="Select fasta file from DM">     
+                    <options from_data_table="all_fasta">
+                        <filter column="2" type="sort_by" />
+                        <validator message="No genomes are available for the selected input dataset" type="no_options" />
+                    </options>
+                </param>
+            </when>
+        </conditional> 
+        <param name="test" type="hidden"/>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="input">
+                <param name="is_select" value="fastx"/>
+                <param name="from_dm" value="phiX174"/>
+            </conditional>
+            <param name="test" value="fasle"></param>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text='"format_version":"3"'/>
+                    <has_text text='"name":"phiX174.fasta (k=31, w=15)"'/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="input">
+                <param name="is_select" value="prebuilt"/>
+                <param name="download" value="human"/>
+            </conditional>
+            <param name="test" value="true"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text='"format_version":"3"'/>
+                    <has_text text='"name":"panhuman-1 (k=31, w=15)"'/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Download prebuilt index files for deacon or download other index files made for deacon via url.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1101/2025.06.09.658732</citation>
+    </citations>
+</tool>

data_managers/data_manager_deacon/data_manager_conf.xml

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+<data_managers>
+    <data_manager tool_file="data_manager/deacon_datamanager.xml" id="deacon_build_database">
+        <data_table name="deacon">
+            <output>
+                <column name="value"/>
+                <column name="dbkey"/>
+                <column name="name"/>
+                <column name="version"/>
+                <column name="path" output_ref="out_file">
+                    <move type="file">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">deacon/${value}/${path}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/deacon/${value}/${path}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+                <column name="format_version"/>
+                <column name="note"/>
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>

data_managers/data_manager_deacon/test-data/all_fasta.loc

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+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>		<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
+phiX174	phiX174	phiX174	${__HERE__}/phiX174.fasta

data_managers/data_manager_deacon/test-data/deacon.loc

@@ -0,0 +1,3 @@
+db_download_xxxx-xx-xx		deacon human index db	0.12.0	/tmp/tmpf_hplx2a/galaxy-dev/tool-data/deacon/0.12.0/test.idx	3	Testing
+custom-2026-07-09		phiX174.fasta (k=31, w=15)	0.12.0	/mnt/d/arbeit/galaxy/tool-data/deacon/custom-2026-07-09/phiX174.fasta.idx	3	Build from fasta file phiX174.fasta
+prebuilt-2026-07-09		panhuman-1 (k=31, w=15)	0.12.0	/mnt/d/arbeit/galaxy/tool-data/deacon/prebuilt-2026-07-09/panhuman-1.k31w15.idx	3	Prebuilt index files from the devs of deacon

data_managers/data_manager_deacon/test-data/phiX174.fasta

@@ -0,0 +1,78 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA

data_managers/data_manager_deacon/tool-data/all_fasta.loc.sample

@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>		<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#

data_managers/data_manager_deacon/tool-data/deacon.loc.sample

@@ -0,0 +1,9 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a the deacon dabase.
+#
+#<unique_build_id>  <dbkey>  <display_name>	<version>	<file_base_path>	<index_format_version>	<note_like_who_did_create_the_db>
+
+#The <version> column indicates the deacon version that generated the database
+
+#
+#deacon_db		Deacon_database	0.12.0	/mnt/galaxyIndices/deacon_database/test.idx	3	just for the test

data_managers/data_manager_deacon/tool_data_table_conf.xml.sample

@@ -0,0 +1,6 @@
+<tables>
+    <table name="deacon" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, version, path, format_version, note</columns>
+        <file path="tool-data/deacon.loc" />
+    </table>
+</tables>

data_managers/data_manager_deacon/tool_data_table_conf.xml.test

@@ -0,0 +1,12 @@
+<tables>
+    <!-- Location of deacon indexes for testing -->
+    <table name="deacon" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, version, path, format_version, note</columns>
+        <file path="${__HERE__}/test-data/deacon.loc" />
+    </table>   
+<!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+</tables>

tools/deacon/.shed.yml

@@ -0,0 +1,13 @@
+name: deacon
+owner: iuc
+description: filters DNA sequences in FASTA/Q files and streams using accelerated minimizer comparison
+homepage_url: https://github.com/bede/deacon
+long_description: |
+  Filter sequences using accelerated minimizer comparison with query sequence(s), 
+  emitting either matching sequences (search mode), or sequences without matches (deplete mode). 
+  Sequences match when they share enough distinct minimizers with the indexed query to exceed chosen 
+  absolute and relative thresholds.
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/deacon
+type: unrestricted
+categories: 
+- Metagenomics