diff metaphlan2.xml @ 2:f60773e921fa draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit bfc25b2695b9689c60101f84162610194a33c886"

--- a/metaphlan2.xml	Fri Mar 19 09:38:42 2021 +0000
+++ b/metaphlan2.xml	Fri Mar 19 21:39:32 2021 +0000
@@ -34,7 +34,13 @@
 #end if
 
 metaphlan2.py
-    '$input_file'
+    #if $input_file.datatype.file_ext.endswith(".gz")
+        <(zcat '$input_file')
+    #else if $input_file.datatype.file_ext.endswith(".bz2")
+        <(bzcat '$input_file')
+    #else
+        '$input_file'
+    #end if
     -o '$output_file'
     --input_type $ext
     --bowtie2_exe `which bowtie2`
@@ -74,7 +80,7 @@
     ]]></command>
 
     <inputs>
-        <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file"/>
+        <param name="input_file" type="data" format="fastq,fastq.gz,fastq.bz2,fasta,fasta.gz,fasta.bz2,sam" label="Input file"/>
         <conditional name="db">
             <param name="db_selector" type="select" label="Database with clade-specific marker genes">
                 <option value="cached" selected="true">Locally cached</option>
@@ -133,10 +139,10 @@
 
     <tests>
         <test>
-            <param name="input_file" value="input_sequences.fasta"/>
+            <param name="input_file" value="input_sequences.fasta" ftype="fasta"/>
             <param name="db_selector" value="history" />
             <param name="mpa_pkl" value="marker_metadata.json" />
-            <param name="bowtie2db" value="marker_sequences.fasta" />
+            <param name="bowtie2db" value="marker_sequences.fasta"  ftype="fasta"/>
             <param name="analysis_type_select" value="rel_ab" />
             <param name="taxonomic_level" value="a" />
             <param name="min_cu_len" value="2000" />
@@ -146,7 +152,23 @@
             <param name="ignore_bacteria" value="" />
             <param name="ignore_archaea" value="" />
             <param name="stat_q" value="0.1" />
-            <output name="output_file" file="community_profile.tabular"/>
+            <output name="output_file" file="community_profile.tabular" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input_file" value="input_sequences.fastq.gz" ftype="fastqsanger.gz"/>
+            <param name="db_selector" value="history" />
+            <param name="mpa_pkl" value="marker_metadata.json" />
+            <param name="bowtie2db" value="marker_sequences.fasta"  ftype="fasta"/>
+            <param name="analysis_type_select" value="rel_ab" />
+            <param name="taxonomic_level" value="a" />
+            <param name="min_cu_len" value="2000" />
+            <param name="min_alignment_len" value="0" />
+            <param name="ignore_viruses" value="" />
+            <param name="ignore_eukaryotes" value="" />
+            <param name="ignore_bacteria" value="" />
+            <param name="ignore_archaea" value="" />
+            <param name="stat_q" value="0.1" />
+            <output name="output_file" file="community_profile.tabular" ftype="tabular"/>
         </test>
     </tests>