From 7127d7a93456a3d0c1b6f16d9a11cfc5c5882ffa Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Thu, 26 Sep 2024 12:25:29 +0000
Subject: [PATCH 1/2] Updating tools/humann from version 3.8 to 3.9

---
 tools/humann/macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/humann/macros.xml b/tools/humann/macros.xml
index 97cc121b0d0..9d950a7c35e 100644
--- a/tools/humann/macros.xml
+++ b/tools/humann/macros.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">3.8</token>
+    <token name="@TOOL_VERSION@">3.9</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="edam_ontology">

From a4e266b49ca33d08b886a52dc0845dc33a4a608b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= <berenice.batut@gmail.com>
Date: Thu, 26 Sep 2024 16:24:10 +0200
Subject: [PATCH 2/2] Remove wrappers of removed commands

---
 tools/humann/humann_associate.xml       |  77 ----------------
 tools/humann/humann_rna_dna_norm.xml    | 117 ------------------------
 tools/humann/humann_strain_profiler.xml |  68 --------------
 3 files changed, 262 deletions(-)
 delete mode 100644 tools/humann/humann_associate.xml
 delete mode 100644 tools/humann/humann_rna_dna_norm.xml
 delete mode 100644 tools/humann/humann_strain_profiler.xml

diff --git a/tools/humann/humann_associate.xml b/tools/humann/humann_associate.xml
deleted file mode 100644
index 5cfa4ba2de5..00000000000
--- a/tools/humann/humann_associate.xml
+++ /dev/null
@@ -1,77 +0,0 @@
-<tool id="humann_associate" name="Perform metadata association" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>on HUMAnN generated table</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="edam_ontology"/>
-    <expand macro="requirements"/>
-    <expand macro="version"/>
-    <command detect_errors="exit_code"><![CDATA[
-humann_associate
-    --input '$input'
-    --focal-metadatum '$focal_metadatum'
-    --last-metadatum '$last_metadatum'
-    --focal-type '$focal_type'
-    --fdr $fdr
-    --output '$output'
-    ]]></command>
-    <inputs>
-        <param argument="--input" type="data" format="tsv,tabular" label="Gene family or pathway table with metadata rows at the top"/>
-        <param argument="--focal-metadatum" type="text" value="" label="Metadatum to test vs. community feature totals">
-            <sanitizer invalid_char="">
-                <valid initial="string.ascii_letters,string.digits">
-                    <add value="_" />
-                </valid>
-            </sanitizer>
-            <validator type="empty_field" />
-        </param>
-        <param argument="--last-metadatum" type="text" value="" label="End of metadata rows">
-            <sanitizer invalid_char="">
-                <valid initial="string.ascii_letters,string.digits">
-                    <add value="_" />
-                </valid>
-            </sanitizer>
-            <validator type="empty_field" />
-        </param>
-        <param argument="--focal-type" type="select" label="Metadatum type">
-            <option value="continuous">Continuous</option>
-            <option value="categorical">Categorical</option>
-        </param>
-        <param argument="--fdr" type="float" value="0.2" label="FDR threshold"/>
-    </inputs>
-    <outputs>
-        <data format="tabular" name="output"/>
-    </outputs>
-    <tests>
-        <test expect_num_outputs="1">
-            <param name="input" value="hmp_pathabund.txt"/>
-            <param name="focal_metadatum" value="STSite"/>
-            <param name="last_metadatum" value="STSite"/>
-            <param name="focal_type" value="categorical"/>
-            <param name="fdr" value="0.2"/>
-            <output name="output" ftype="tabular">
-                <assert_contents>
-                    <has_text text="Feature"/>
-                    <has_text text="BRANCHED-CHAIN-AA-SYN-PWY: superpathway of branched amino acid biosynthesis"/>
-                    <has_text text="Level means (|ed)"/>
-                    <has_text text="P-value"/>
-                    <has_text text="Q-value"/>
-                    <has_n_columns n="4"/>
-                </assert_contents>
-            </output>
-        </test>
-    </tests>
-    <help><![CDATA[
-@HELP_HEADER@
-
-When associating metadata with HUMAnN features, it is often beneficial to associate with community totals and avoid testing each 
-individual feature stratification (to improve statistical power).
-
-This is the approach used by this tool, which can compare feature totals across samples with 
-1) a single continuous metadatum (via the Spearman Correlation) or 
-2) a single categorical metadatum (via the Kruskal-Wallis H-test).
-
-Notably, this is a naive approach to association, but it is useful for tutorial purposes.
-    ]]></help>
-    <expand macro="citations"/>
-</tool>
diff --git a/tools/humann/humann_rna_dna_norm.xml b/tools/humann/humann_rna_dna_norm.xml
deleted file mode 100644
index 624489dae23..00000000000
--- a/tools/humann/humann_rna_dna_norm.xml
+++ /dev/null
@@ -1,117 +0,0 @@
-<tool id="humann_rna_dna_norm" name="Normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description> combined meta'omic sequencing data</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="edam_ontology"/>
-    <expand macro="requirements"/>
-    <expand macro="version"/>
-    <command detect_errors="exit_code"><![CDATA[
-humann_rna_dna_norm
-    --input_dna '$input_dna'
-    --input_rna '$input_rna'
-    --output_basename 'results'
-    --method '$method'
-#if $log.log_transform == 'yes'
-    --log_transform
-    --log_base $log.log_base
-#end if
-    ]]></command>
-    <inputs>
-        <param argument="--input_dna" type="data" format="tsv,tabular,biom1" label="Original DNA output table"/>
-        <param argument="--input_rna" type="data" format="tsv,tabular,biom1" label="Original RNA output table"/>
-        <param argument="--method" type="select" label="Choice of smoothing method">
-            <option value="laplace">Laplace</option>
-            <option value="witten_bell">Witten-Bell</option>
-        </param>
-        <conditional name="log">
-            <param argument="--log_transform" type="select" label="Report log-transformed relative expression values?">
-                <option value="yes">Yes</option>
-                <option value="no">No</option>
-            </param>
-            <when value="yes">
-                <param argument="--log_base" type="integer" value="2" label="Base for log transformation"/>
-            </when>
-            <when value="no"/>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data format="tabular" name="relative_expression" from_work_dir="results-relative_expression.tsv" label="${tool.name} on ${on_string}: Normalized RNA"/>
-        <data format="tabular" name="smoothed_dna" from_work_dir="results-smoothed_dna.tsv" label="${tool.name} on ${on_string}: Smoothed DNA"/>
-        <data format="tabular" name="smoothed_rna" from_work_dir="results-smoothed_rna.tsv" label="${tool.name} on ${on_string}: Smoothed RNA"/>
-    </outputs>
-    <tests>
-        <test expect_num_outputs="3">
-            <param name="input_dna" value="rna_dna_norm-dna.txt"/>
-            <param name="input_rna" value="rna_dna_norm-rna.txt"/>
-            <param name="method" value="laplace"/>
-            <conditional name="log">
-                <param name="log_transform" value="no"/>
-            </conditional>
-            <output name="relative_expression" ftype="tabular">
-                <assert_contents>
-                    <has_text text="A|1"/>
-                    <has_text text="0.285714"/>
-                    <has_n_columns n="3"/>
-                </assert_contents>
-            </output>
-            <output name="smoothed_dna" ftype="tabular">
-                <assert_contents>
-                    <has_text text="A|1"/>
-                    <has_text text="13"/>
-                    <has_n_columns n="3"/>
-                </assert_contents>
-            </output>
-            <output name="smoothed_rna" ftype="tabular">
-                <assert_contents>
-                    <has_text text="A|1"/>
-                    <has_text text="62"/>
-                    <has_n_columns n="3"/>
-                </assert_contents>
-            </output>
-        </test>
-        <test expect_num_outputs="3">
-            <param name="input_dna" value="rna_dna_norm-dna.txt"/>
-            <param name="input_rna" value="rna_dna_norm-rna.txt"/>
-            <param name="method" value="witten_bell"/>
-            <conditional name="log">
-                <param name="log_transform" value="yes"/>
-                <param name="log_base" value="2"/>
-            </conditional>
-            <output name="relative_expression" ftype="tabular">
-                <assert_contents>
-                    <has_text text="A|1"/>
-                    <has_text text="0.118644"/>
-                    <has_n_columns n="3"/>
-                </assert_contents>
-            </output>
-            <output name="smoothed_dna" ftype="tabular">
-                <assert_contents>
-                    <has_text text="A|1"/>
-                    <has_text text="9.24"/>
-                    <has_n_columns n="3"/>
-                </assert_contents>
-            </output>
-            <output name="smoothed_rna" ftype="tabular">
-                <assert_contents>
-                    <has_text text="A|1"/>
-                    <has_text text="39.4545"/>
-                    <has_n_columns n="3"/>
-                </assert_contents>
-            </output>
-        </test>
-    </tests>
-    <help><![CDATA[
-@HELP_HEADER@
-
-Given a DNA table and a RNA table, this tool produces smoothed RNA and DNA values as well as relative expression values. 
-
-"Smoothing" means substituting a small value in place of a zero or missing value. 
-The default method used is "Laplace" (pseudocount) scaling, where the pseudocount is the sample-specific minimum non-zero value (Witten-Bell smoothing is also implemented.)
-
-The DNA and RNA columns must be 1:1 and in the same order.
-
-If working with stratified data, smoothing is carried out on the stratified values and then community totals are recomputed.
-    ]]></help>
-    <expand macro="citations"/>
-</tool>
diff --git a/tools/humann/humann_strain_profiler.xml b/tools/humann/humann_strain_profiler.xml
deleted file mode 100644
index f9a07a461f3..00000000000
--- a/tools/humann/humann_strain_profiler.xml
+++ /dev/null
@@ -1,68 +0,0 @@
-<tool id="humann_strain_profiler" name="Make strain profiles" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description></description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="edam_ontology"/>
-    <expand macro="requirements"/>
-    <expand macro="version"/>
-    <command detect_errors="exit_code"><![CDATA[
-humann_strain_profiler
-    --input '$input'
-    --critical_mean $critical_mean
-    --critical_count $critical_count
-    --pinterval $pinterval_1 $pinterval_2
-    --critical_samples $critical_samples
-#if str($limit) != ''
-    --limit '$limit'
-#end if
-    ]]></command>
-    <inputs>
-        <param argument="--input" type="data" format="tsv,tabular,biom1" label="Merged gene families output for two or more samples"/>
-        <param argument="--critical_mean" type="float" value="10.0" label="Default mean non-zero gene abundance for inclusion"/>
-        <param argument="--critical_count" type="integer" value="500" label="Default non-zero number of genes for inclusion"/>
-        <param name="pinterval_1" type="float" value="1e-10" label="Low prevalence threshold" help="Only genes with prevalence higher than the threshold are allowed"/>
-        <param name="pinterval_2" type="float" value="1" label="High prevalence threshold" help="Only genes with prevalence lower than the threshold are allowed"/>
-        <param argument="--critical_samples" type="integer" value="2" label="Threshold number of samples having strain"/>
-        <param argument="--limit" type="text" value="" optional="true" label="Limit output to species matching a particular pattern?" help="e.g. 'Streptococcus'"/>
-    </inputs>
-    <outputs>
-        <collection name="output" type="list">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)-strain_profile.tsv" format="tabular" directory="."/>
-        </collection>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" value="strain_profiler-input.txt"/>
-            <param name="critical_mean" value="1"/>
-            <param name="critical_count" value="2"/>
-            <param name="pinterval_1" value="1e-10"/>
-            <param name="pinterval_2" value="1"/>
-            <param name="critical_samples" value="2"/>
-            <output_collection name="output" type="list">
-                <element name="s1" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="A|g1.s1"/>
-                        <has_text text="10.0"/>
-                        <has_n_columns n="4"/>
-                    </assert_contents>
-                </element>
-                <element name="s2" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="A|g1.s2"/>
-                        <has_text text="10.0"/>
-                        <has_n_columns n="4"/>
-                    </assert_contents>
-                </element>
-            </output_collection>
-        </test>
-    </tests>
-    <help><![CDATA[
-@HELP_HEADER@
-
-This tool makes strain profiles, based on the principle of detecting variable 
-presence and absence of gene families within a species
-that is otherwise well-covered in multiple samples.
-    ]]></help>
-    <expand macro="citations"/>
-</tool>