diff metaphlan2.xml @ 27:fb2dc25a832d draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty

--- a/metaphlan2.xml	Thu Mar 31 05:45:29 2016 -0400
+++ b/metaphlan2.xml	Tue Apr 12 03:07:32 2016 -0400
@@ -21,7 +21,7 @@
 
     <version_command>
 <![CDATA[
-python \${METAPHLAN2_DIR}/metaphlan2.py -v
+metaphlan2.py -v
 ]]>
     </version_command>
 
@@ -31,15 +31,21 @@
 
         &&
 
-        python \${METAPHLAN2_DIR}/metaphlan2.py
+        metaphlan2.py
             $input_file
             -o $output_file
 
             --input_type ${input_file.datatype.file_ext}
-            --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl 
+
+            #set $data_table = dict([(_[0], _[2]) for _ in $mpa_pkl.input.options.tool_data_table.data])
+            #set $db = $mpa_pkl.value
+            --mpa_pkl $data_table[$db]
 
             --bowtie2_exe `which bowtie2`
-            --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200
+
+            #set $data_table = dict([(_[0], _[2]) for _ in $bowtie2db.input.options.tool_data_table.data])
+            #set $db = $bowtie2db.value
+            --bowtie2db $data_table[$db]
 
             --no_map
 
@@ -75,6 +81,14 @@
     <inputs>
         <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/>
 
+        <param name="mpa_pkl" label="Metadata" type="select" >
+            <options from_data_table="metaphlan2_metadata" />
+        </param>
+
+        <param name="bowtie2db" label="BowTie2 database" type="select" >
+            <options from_data_table="metaphlan2_bowtie_db" />
+        </param>
+
         <conditional name="analysis_type">
             <param name="analysis_type_select" type="select" label="Type of analysis to perform">
               <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
@@ -142,6 +156,8 @@
     <tests>
         <test>
             <param name="input_file" value="metaphlan2_input_sequences.fastq"/>
+            <param name="mpa_pkl" value="" />
+            <param name="bowtie2db" value="" />
             <param name="analysis_type_select" value="rel_ab" />
             <param name="taxonomic_level" value="a" />
             <param name="min_cu_len" value="2000" />
@@ -152,9 +168,8 @@
             <param name="ignore_archaea" value="" />
             <param name="stat_q" value="0.1" />
             <param name="sam_output" value='false' />
-            <param name="biom_output" value='true' />
+            <param name="biom_output" value='false' />
             <output name="output_file" file="metaphlan2_profiled_metagenome.txt"/>
-            <output name="biom_output_file" file="metaphlan2_biom.biom"/>
         </test>
     </tests>