# HG changeset patch
# User iuc
# Date 1616914870 0
# Node ID cda49fede0c20d95cddef8b2815b0d7bafdae21e
# Parent  bb13650e81159a68c3a4131c5ca0235838790aa3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 8d953926efdf23d8c3fb8719341dff51a55a92f2"

diff -r bb13650e8115 -r cda49fede0c2 humann2.xml
--- a/humann2.xml	Fri Feb 05 18:28:51 2021 +0000
+++ b/humann2.xml	Sun Mar 28 07:01:10 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="humann2" name="HUMAnN2" version="@WRAPPER_VERSION@.2">
+<tool id="humann2" name="HUMAnN2" version="@WRAPPER_VERSION@.3">
     <description>to profile presence/absence and abundance of microbial pathways and gene families</description>
     <macros>
         <import>humann2_macros.xml</import>
@@ -50,8 +50,28 @@
     #end if
 #end if
 
+#if $input.ext.startswith("fasta")
+    #set ext="fasta"
+#else if $input.ext.startswith("fastq")
+    #set ext="fastq"
+#else if $input.ext.endswith("bam")
+    #set ext="bam"
+#else if $input.ext == 'sam'
+    #set ext="sam"
+#else if $input.ext == 'biom1'
+    #set ext="biom"
+#else
+    >&2 "unknown extension $input.ext"
+    exit 1; 
+#end if
+
+#if $input.ext.endswith(".gz")
+    #set ext+=".gz"
+#end if
+
 humann2
     --input '$input'
+    --input-format $ext
     -o 'output'
     $bypass.bypass_prescreen
     $bypass.bypass_nucleotide_index
@@ -111,7 +131,7 @@
     $adv.remove_column_description_output
     ]]></command>
     <inputs>
-        <param argument="--input" type="data" format="fastq,fasta,sam,bam,biom1" label="Input sequence file"/>
+        <param argument="--input" type="data" format="fastq,fastq.gz,fasta,fasta.gz,sam,bam,biom1" label="Input sequence file"/>
         <section name="bypass" title="Options to bypass some steps" expanded="False">
             <param name="bypass_prescreen" argument="--bypass-prescreen" type="boolean" truevalue="--bypass-prescreen" falsevalue="" checked="false" label="Bypass the prescreen step and run on the full ChocoPhlAn database?"/>
             <param name="bypass_nucleotide_index" argument="--bypass-nucleotide-index" type="boolean" truevalue="--bypass-nucleotide-index" falsevalue="" checked="false" label="Bypass the nucleotide index step and run on the indexed ChocoPhlAn database?"/>
@@ -283,7 +303,7 @@
             </output>
         </test>
         <test>
-            <param name="input" value="input_sequences.fasta"/>
+            <param name="input" value="input_sequences.fastq.gz"/>
             <param name="bypass_prescreen" value=""/>
             <param name="bypass_nucleotide_index" value=""/>
             <param name="bypass_translated_search" value=""/>
diff -r bb13650e8115 -r cda49fede0c2 test-data/input_sequences.fasta
--- a/test-data/input_sequences.fasta	Fri Feb 05 18:28:51 2021 +0000
+++ b/test-data/input_sequences.fasta	Sun Mar 28 07:01:10 2021 +0000
@@ -75,7 +75,8 @@
 >r495|637000026.fna|898444|898595|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln166_#0/1
 GTAACTGGAGTATCTTACAAAAGACTGAAAAGACAATTTCTCTTACAATATTCCTGTTACTCTTTATCCTTGGAGTATCCATTGGCTCTAATAGCCTGATTGTGAATAATCTCGGTAAGTTTGGATGGCAGGCGATCATTCTTGCCGTATC
 >r497|641736196.fna|48795|48946|_from_ |NZ_ABFZ02000020_Bacteroides_stercoris_ATCC_43183,|_ln354_#0/1
-TTGCCATCCCGCTCCCGTGCAAGGACTCCACACCTTTAAGATTCTGTCGAGCCACGGCAAGTTCCGATTGCAAAGAACTCAATTCGACCGAACGTATATCTACCATCCTTTTACCTTTTTCTGCATAATCGCCAAGTGAAAAGTAGCTTTT>r2|637000026.fna|5753889|5754040|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln383_#0/1
+TTGCCATCCCGCTCCCGTGCAAGGACTCCACACCTTTAAGATTCTGTCGAGCCACGGCAAGTTCCGATTGCAAAGAACTCAATTCGACCGAACGTATATCTACCATCCTTTTACCTTTTTCTGCATAATCGCCAAGTGAAAAGTAGCTTTT
+>r2|637000026.fna|5753889|5754040|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln383_#0/1
 CTCCGTCCGCTGGTAGAACGTCTGGTAGAAGCTCAAAAAGCATTGGCAACCAAATACCTTTCCGAAGCCAAACGACTGATTGCCTCCAACGACAAGAAGGAAGTGGAAGAAGGATTCCTTGCCCTTTATCGTAGCCACAAGTGTCTTCCGA
 >r3|637000026.fna|1749333|1749484|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln165_#0/1
 AAGTAAAAGTCTACACACAGGAAGGAACGATAATGGAAAGTACGATTGAAGTAAATCGTCCGATGGAGATAGCAGGATGGAAAATTTATCAGCTTAGTTATGATGAGTCGAAAGGTCGCTGGAGCGATATCAGTGTCTTTGAGCTGGTTCG
diff -r bb13650e8115 -r cda49fede0c2 test-data/input_sequences.fastq.gz
Binary file test-data/input_sequences.fastq.gz has changed