# HG changeset patch
# User iuc
# Date 1770226189 0
# Node ID 229eef1c5498eac146a00320ee0644de46c977df
# Parent  9152525e3c739bfa50a183e80c74b6ca14001828
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann commit f434c096f244d1ff01a3e439bfdf8ef3999d75af

diff -r 9152525e3c73 -r 229eef1c5498 humann.xml
--- a/humann.xml	Fri Sep 27 09:57:04 2024 +0000
+++ b/humann.xml	Wed Feb 04 17:29:49 2026 +0000
@@ -1,4 +1,4 @@
-<tool id="humann" name="HUMAnN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="humann" name="HUMAnN" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>to profile presence/absence and abundance of microbial pathways and gene families</description>
     <macros>
         <import>macros.xml</import>
@@ -170,21 +170,25 @@
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
 #import re
-#if $in.input.ext.startswith("fasta")
+#if $input_conditional.input.ext.startswith("fasta")
     #set ext="fasta"
-#else if $in.input.ext.startswith("fastq")
+#else if $input_conditional.input.ext.startswith("fastq")
     #set ext="fastq"
-#else if $in.input.ext.endswith("bam")
+#else if $input_conditional.input.ext.endswith("bam")
     #set ext="bam"
-#else if $in.input.ext == 'sam'
+#else if $input_conditional.input.ext == 'sam'
     #set ext="sam"
-#else if $in.input.ext == 'biom1'
+#else if $input_conditional.input.ext == 'biom1'
     #set ext="biom"
+#else if $input_conditional.input.ext == 'tabular'
+    #set ext="genetable"
+#else if $input_conditional.input.ext == 'tsv'
+    #set ext="genetable"
 #else
-    >&2 "unknown extension $in.input.ext"
+    >&2 "unknown extension $input_conditional.input.ext"
     exit 1; 
 #end if
-#if $in.input.ext.endswith(".gz")
+#if $input_conditional.input.ext.endswith(".gz")
     #set ext+=".gz"
 #end if
 
@@ -209,7 +213,7 @@
 #end if
 
 humann
-    --input '$input'
+    --input '$input_conditional.input'
     --input-format $ext
     -o 'output'
 #if $wf.selector == 'bypass_prescreen'
@@ -255,7 +259,7 @@
     --memory-use minimum
     ]]></command>
     <inputs>
-        <conditional name="in">
+        <conditional name="input_conditional">
             <param name="selector" type="select" label="Input(s)">
                 <option value="raw" selected="true">Quality-controlled shotgun sequencing reads (metagenome (DNA reads) or metatranscriptome (RNA reads))</option>
                 <option value="mapping">Pre-computed mappings of reads to database sequences</option>
@@ -350,10 +354,10 @@
     </inputs>
     <outputs>
         <data name="gene_families_tsv" format="tabular" from_work_dir="output/*_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" >
-            <filter>out['output_format'] == "tsv"</filter>
+            <filter>input_conditional['selector'] != "abundance" and out['output_format'] == "tsv"</filter>
         </data>
         <data name="gene_families_biom" format="biom1" from_work_dir="output/*_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance as biom">
-            <filter>out['output_format'] == "biom"</filter>
+            <filter>input_conditional['selector'] != "abundance" and out['output_format'] == "biom"</filter>
         </data>
         <data name="pathcoverage_tsv" format="tabular" from_work_dir="output/*_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways and their coverage" >
             <filter>out['output_format'] == "tsv"</filter>
@@ -396,7 +400,7 @@
     <tests>
         <!-- This test refers to the Metaphlan v3 DB format, and hence should fail, which is to be caught gracefully. -->
         <test expect_exit_code="42" expect_failure="true">
-            <conditional name="in">
+            <conditional name="input_conditional">
                 <!-- raw fasta file -->
                 <param name="selector" value="raw"/>
                 <param name="input" value="demo.fastq.gz"/>
@@ -427,7 +431,7 @@
         </test>
         <!-- This test refers to the Metaphlan v4 DB format, and hence should be a straight pass. -->
         <test expect_num_outputs="12">
-            <conditional name="in">
+            <conditional name="input_conditional">
                 <!-- raw fasta file -->
                 <param name="selector" value="raw"/>
                 <param name="input" value="demo.fastq.gz"/>
@@ -580,7 +584,7 @@
             </output>
         </test>
         <test expect_num_outputs="4">
-            <conditional name="in">
+            <conditional name="input_conditional">
                 <!-- fastq file -->
                 <param name="selector" value="raw"/>
                 <param name="input" value="demo.fasta.gz"/>
@@ -660,7 +664,7 @@
             </output>
         </test>
         <test expect_num_outputs="4">
-            <conditional name="in">
+            <conditional name="input_conditional">
                 <param name="selector" value="raw"/>
                 <param name="input" value="demo.fasta.gz"/>
             </conditional>
@@ -742,7 +746,7 @@
             </output>
         </test>
         <test expect_num_outputs="4">
-            <conditional name="in">
+            <conditional name="input_conditional">
                 <!-- mapping SAM file -->
                 <param name="selector" value="mapping"/>
                 <param name="input" value="demo.sam"/>
@@ -814,8 +818,40 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Test abundance input table -->
+        <test expect_num_outputs="3">
+            <conditional name="input_conditional">
+                <param name="selector" value="abundance"/>
+                <param name="input" value="demo_genefamilies.tsv"/>
+            </conditional>
+            <output name="pathcoverage_tsv" ftype="tabular">
+                <assert_contents>
+                    <has_text text="UNMAPPED"/>
+                    <has_text text="UNINTEGRATED"/>
+                    <has_text text="PWY-5423"/>
+                    <has_n_columns n="2"/>
+                    <has_n_lines n="8"/>
+                </assert_contents>
+            </output>
+            <output name="pathabundance_tsv" ftype="tabular">
+                <assert_contents>
+                    <has_text text="UNMAPPED"/>
+                    <has_text text="UNINTEGRATED"/>
+                    <has_text text="PWY-5423"/>
+                    <has_n_columns n="2"/>
+                    <has_n_lines n="8"/>
+                </assert_contents>
+            </output>
+            <output name="log" ftype="txt">
+                <assert_contents>
+                    <has_text text="processing gene table"/>
+                    <has_text text="g__Bacteroides.s__Bacteroides_vulgatus"/>
+                    <has_text text="computing pathways"/>
+                </assert_contents>
+            </output>
+        </test>
         <test expect_num_outputs="4">
-            <conditional name="in">
+            <conditional name="input_conditional">
                 <!-- raw fasta file -->
                 <param name="selector" value="raw"/>
                 <param name="input" value="demo.fastq.gz"/>
@@ -880,7 +916,7 @@
             </output>
         </test>
         <test expect_num_outputs="4">
-            <conditional name="in">
+            <conditional name="input_conditional">
                 <!-- raw fasta file -->
                 <param name="selector" value="raw"/>
                 <param name="input" value="demo.fastq.gz"/>
@@ -956,7 +992,7 @@
         </test>
         <!-- This test should fail for as metaphlan v4 is invoked on outdated input DB. -->
         <test expect_exit_code="1" expect_failure="true">
-            <conditional name="in">
+            <conditional name="input_conditional">
                 <!-- raw fasta file -->
                 <param name="selector" value="raw"/>
                 <param name="input" value="demo.fastq.gz"/>