# HG changeset patch
# User galaxy-australia
# Date 1671491630 0
# Node ID 767e50ca160eaffe526eb403e3d4f010d672793b
# Parent  aaa924525210903b0af44dc178d628b1c85f51e7
Deleted all files

diff -r aaa924525210 -r 767e50ca160e gtdbtk_classify_wf.xml
--- a/gtdbtk_classify_wf.xml	Mon Dec 19 07:03:08 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,156 +0,0 @@
-<tool id="gtdbtk_classify_wf" name="GTDB-Tk Classify genomes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>by placement in GTDB reference tree</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements"/>
-    <command detect_errors="exit_code"><![CDATA[
-#import re
-
-mkdir input_dir &&
-mkdir output_dir &&
-mkdir output_tsv_dir &&
-mkdir output_newick_dir &&
-mkdir output_fasta_dir &&
-#for $i in $input:
-    ## gtdbtk uses the file extension to determine the input format.
-    #set ext = "." + $i.ext
-    #set input_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) + $ext
-    ln -s '${i}' input_dir/'${input_identifier}' &&
-#end for
-export GTDBTK_DATA_PATH=$gtdbtk_db.fields.path &&
-gtdbtk classify_wf
---genome_dir input_dir
---extension '$ext'
---out_dir output_dir
---cpus \${GALAXY_SLOTS:-4}
---min_perc_aa $advanced.min_perc_aa
-$advanced.force
---min_af $advanced.min_af
-#if str($advanced.output_process_log) == 'yes':
-    && cat output_dir/gtdbtk.warnings.log output_dir/gtdbtk.log > '$process_log'
-#end if
-    ]]></command>
-    <inputs>
-        <param name="input" type="data" format="fasta,fasta.gz" multiple="true" label="Fasta (Genome) files"/>
-        <param name="gtdbtk_db" type="select" label="GTDB-Tk database">
-            <options from_data_table="gtdbtk_database">
-                <validator type="no_options" message="No locally cached GTDB-Tk database is available"/>
-            </options>
-        </param>
-        <section name="advanced" title="Advanced options">
-            <param argument="--min_perc_aa" type="integer" min="0" max="100" value="10" label="Exclude genomes that do not have at least this percentage of AA in the MSA" help="Inclusive bound"/>
-            <param argument="--force" type="boolean" truevalue="--force" falsevalue="" checked="false" label="Continue processing if an error occurs on a single genome?"/>
-            <param argument="--min_af" type="float" min="0" max="1" value="0.65" label="Minimum alignment fraction to consider closest genome"/>
-            <param name="output_process_log" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output process log file?"/>
-        </section>
-    </inputs>
-    <outputs>
-        <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
-            <filter>advanced['output_process_log'] == 'yes'</filter>
-        </data>
-        <collection name="output_tsv" type="list" format="tsv" label="${tool.name} on ${on_string} (tsv)">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" ext="tsv" directory="output_dir"/>
-        </collection>
-        <collection name="output_newick" type="list" format="newick" label="${tool.name} on ${on_string} (newick)">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tree" ext="newick" directory="output_dir"/>
-        </collection>
-        <collection name="output_fasta" type="list" format="fasta" label="${tool.name} on ${on_string} (fasta)">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta" ext="fasta" directory="output_dir"/>
-        </collection>
-    </outputs>
-    <tests>
-        <!-- The commented test here is valid if we could store the GTDB-Tk database -->
-        <!--
-        <test expect_num_outputs="3">
-            <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/>
-            <param name="gtdbtk_db" value="gtdbtk202"/>
-            <output_collection name="output_tsv" type="list" count="6">
-                <element name="gtdbtk.ar122.filtered" ftype="tsv">
-                    <assert_contents>
-                        <has_size value="0"/>
-                    </assert_contents>
-                </element>
-                <element name="gtdbtk.ar122.markers_summary" ftype="tsv">
-                    <assert_contents>
-                        <has_text text="number_unique_genes"/>
-                    </assert_contents>
-                </element>
-                <element name="gtdbtk.ar122.summary" ftype="tsv">
-                    <assert_contents>
-                        <has_text text="genome_1_fna_gz"/>
-                    </assert_contents>
-                </element>
-                <element name="gtdbtk.bac120.markers_summary" ftype="tsv">
-                    <assert_contents>
-                        <has_text text="genome_1_fna_gz"/>
-                    </assert_contents>
-                </element>
-                <element name="gtdbtk.failed_genomes" ftype="tsv">
-                    <assert_contents>
-                        <has_size value="0"/>
-                    </assert_contents>
-                </element>
-                <element name="gtdbtk.translation_table_summary" ftype="tsv">
-                    <assert_contents>
-                        <has_text text="genome_1_fna_gz"/>
-                    </assert_contents>
-                </element>
-            </output_collection>
-            <output_collection name="output_newick" type="list" count="1">
-                <element name="gtdbtk.ar122.classify" ftype="newick">
-                    <assert_contents>
-                        <has_text text="GB_GCA_"/>
-                    </assert_contents>
-                </element>
-            </output_collection>
-            <output_collection name="output_fasta" type="list" count="2">
-                <element name="gtdbtk.ar122.msa" ftype="fasta">
-                    <assert_contents>
-                        <has_text text="GB_GCA_000008085"/>
-                    </assert_contents>
-                </element>
-                <element name="gtdbtk.ar122.user_msa" ftype="fasta">
-                    <assert_contents>
-                        <has_text text="genome_1_fna_gz"/>
-                    </assert_contents>
-                </element>
-            </output_collection>
-        </test>
-        -->
-        <!-- GTDB-Tk databases are far too large to test currently -->
-        <test expect_failure="true">
-            <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/>
-            <param name="gtdbtk_db" value="gtdbtk202"/>
-            <assert_stderr>
-                <has_text text="Fatal error: Exit code 1"/>
-            </assert_stderr>
-        </test>
-    </tests>
-    <help><![CDATA[
-**What it does**
-
-GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes
-based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or
-thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also
-be applied to isolate and single-cell genomes. 
-
-This tool accepts one or more fasta (genome) files and determines taxonomic classification of genomes by
-maximum-likelihood (ML) placement.  The classification workflow consists of three steps: identify, align, and
-classify.
-
-The identify step calls genes using Prodigal, and uses HMM models and the HMMER package to identify the 120 bacterial
-and 122 archaeal marker genes used for phylogenetic inference.  Multiple sequence alignments (MSA) are obtained by
-aligning marker genes to their respective HMM model.
-
-The align step concatenates the aligned marker genes and filters the concatenated MSA to approximately 5,000
-amino acids.
-
-Finally, the classify step uses pplacer to find the maximum-likelihood placement of each genome in the GTDB-Tk
-reference tree. GTDB-Tk classifies each genome based on its placement in the reference tree, its relative evolutionary
-divergence, and/or average nucleotide identity (ANI) to reference genomes.
-
-Results can be impacted by a lack of marker genes or contamination. 
-    ]]></help>
-    <expand macro="citations"/>
-</tool>
diff -r aaa924525210 -r 767e50ca160e macros.xml
--- a/macros.xml	Mon Dec 19 07:03:08 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<macros>
-    <token name="@TOOL_VERSION@">2.1.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@PROFILE@">20.09</token>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="@TOOL_VERSION@">gtdbtk</requirement>
-        </requirements>
-    </xml>
-    <xml name="citations">
-        <citations>
-            <citation type="doi">10.1093/bioinformatics/btz848</citation>
-        </citations>
-    </xml>
-</macros>
diff -r aaa924525210 -r 767e50ca160e test-data/genome_1.fna.gz
Binary file test-data/genome_1.fna.gz has changed
diff -r aaa924525210 -r 767e50ca160e test-data/gtdbtk_database.loc
--- a/test-data/gtdbtk_database.loc	Mon Dec 19 07:03:08 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-# This is a sample file distributed with Galaxy that enables tools
-# to use a directory of GTDB-Tk databases.  The gtdbtk_databases.loc
-# file has this format (longer white space characters are TAB characters):
-#
-# <unique_build_id> <display_name>  <directory_path>
-#
-# So, for example, if you have the gtdbtk 202 stored in 
-# /depot/data2/galaxy/gtdbtk/202/, 
-# then the gtdbtk_databases.loc entry would look like this:
-#
-# release202    gtdbtk database release 202 /depot/data2/galaxy/gtdbtk/release202
-#
-# and your /depot/data2/galaxy/gtdbtk/release202 directory
-# would contain GTDB-Tk database files for release 202, sommething like this:
-#
-#drwxr-sr-x  3 gvk G-824019    4096 Apr 20  2021 fastani/
-#-rw-r--r--  1 gvk G-824019 4810764 Apr 22  2021 manifest.tsv
-#drwxr-sr-x  4 gvk G-824019    4096 Apr 21  2021 markers/
-#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 masks/
-#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 metadata/
-#drwxr-sr-x  2 gvk G-824019    4096 Apr 21  2021 mrca_red/
-#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 msa/
-#drwxr-sr-x  4 gvk G-824019    4096 Apr 21  2021 pplacer/
-#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 radii/
-#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 taxonomy/
-gtdbtk202	GTDB-Tk database v202	${__HERE__}/gtdbtk202
diff -r aaa924525210 -r 767e50ca160e tool-data/gtdbtk_database.loc.sample
--- a/tool-data/gtdbtk_database.loc.sample	Mon Dec 19 07:03:08 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-# This is a sample file distributed with Galaxy that enables tools
-# to use a directory of GTDB-Tk databases.  The gtdbtk_databases.loc
-# file has this format (longer white space characters are TAB characters):
-#
-# <unique_build_id> <display_name>  <directory_path>
-#
-# So, for example, if you have the gtdbtk 202 stored in 
-# /depot/data2/galaxy/gtdbtk/202/, 
-# then the gtdbtk_databases.loc entry would look like this:
-#
-# release202    gtdbtk database release 202 /depot/data2/galaxy/gtdbtk/release202
-#
-# and your /depot/data2/galaxy/gtdbtk/release202 directory
-# would contain GTDB-Tk database files for release 202, sommething like this:
-#
-#drwxr-sr-x  3 gvk G-824019    4096 Apr 20  2021 fastani/
-#-rw-r--r--  1 gvk G-824019 4810764 Apr 22  2021 manifest.tsv
-#drwxr-sr-x  4 gvk G-824019    4096 Apr 21  2021 markers/
-#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 masks/
-#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 metadata/
-#drwxr-sr-x  2 gvk G-824019    4096 Apr 21  2021 mrca_red/
-#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 msa/
-#drwxr-sr-x  4 gvk G-824019    4096 Apr 21  2021 pplacer/
-#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 radii/
-#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 taxonomy/
diff -r aaa924525210 -r 767e50ca160e tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Mon Dec 19 07:03:08 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-<tables>
-    <!-- Locations of GTDB-Tk database versions 202 and higher -->
-    <table name="gtdbtk_database" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/gtdbtk_database.loc" />
-    </table>
-</tables>
diff -r aaa924525210 -r 767e50ca160e tool_data_table_conf.xml.test
--- a/tool_data_table_conf.xml.test	Mon Dec 19 07:03:08 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-<tables>
-    <!-- Location of databases for gtdbtk version 202 and higher -->
-    <table name="gtdbtk_database" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="${__HERE__}/test-data/gtdbtk_database.loc" />
-    </table>
-</tables>