# HG changeset patch
# User bebatut
# Date 1460444852 14400
# Node ID fb2dc25a832d964b202d6929522f4188d9e8e338
# Parent  3f52f2d65d41ef1a88c4e0061242a2bf9142e5d6
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty

diff -r 3f52f2d65d41 -r fb2dc25a832d metaphlan2.xml
--- 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>
 
diff -r 3f52f2d65d41 -r fb2dc25a832d metaphlan2krona.xml
--- a/metaphlan2krona.xml	Thu Mar 31 05:45:29 2016 -0400
+++ b/metaphlan2krona.xml	Tue Apr 12 03:07:32 2016 -0400
@@ -21,13 +21,13 @@
 
     <version_command>
 <![CDATA[
-python \${METAPHLAN2_DIR}/utils/metaphlan2krona.py -v
+metaphlan2krona.py -v
 ]]>
     </version_command>
 
     <command>
 <![CDATA[        
-        python \${METAPHLAN2_DIR}/utils/metaphlan2krona.py
+        metaphlan2krona.py
             -p $input_file
             -k $krona
 ]]>
@@ -43,7 +43,11 @@
             label="${tool.name} on ${on_string}: Krona file" />
     </outputs>
 
-    <tests>      
+    <tests>
+        <test>
+            <param name="input_file" value="metaphlan2_profiled_metagenome.txt"/>
+            <output name="krona" file="metaphlan2krona_output_file.txt"/>
+        </test>      
     </tests>
 
     <help><![CDATA[
diff -r 3f52f2d65d41 -r fb2dc25a832d test-data/metaphlan2krona_output_file.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metaphlan2krona_output_file.txt	Tue Apr 12 03:07:32 2016 -0400
@@ -0,0 +1,31 @@
+28.29995		Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	Staphylococcus_aureus
+27.12936		Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	Staphylococcus_epidermidis
+16.29021		Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus	Streptococcus_mutans
+6.70485		Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia	Escherichia_coli
+6.518		Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter	Methanobrevibacter_smithii
+5.59702		Bacteria	Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	Rhodobacter	Rhodobacter_sphaeroides
+4.8513		Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia	Escherichia_unclassified
+1.12042		Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	Pseudomonas_unclassified
+0.9463		Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium	Clostridium_beijerinckii
+0.82072		Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus	Streptococcus_agalactiae
+0.81027		Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	Pseudomonas_aeruginosa
+0.36084		Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium	Propionibacterium_acnes
+0.15821		Bacteria	Deinococcus_Thermus	Deinococci	Deinococcales	Deinococcaceae	Deinococcus	Deinococcus_unclassified
+0.15178		Bacteria	Deinococcus_Thermus	Deinococci	Deinococcales	Deinococcaceae	Deinococcus	Deinococcus_radiodurans
+0.12046		Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter	Acinetobacter_baumannii
+0.07684		Bacteria	Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	Helicobacter	Helicobacter_pylori
+0.04347		Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria	Neisseria_meningitidis
+28.29995		Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	Staphylococcus_aureus	Staphylococcus_aureus_unclassified
+27.12936		Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	Staphylococcus_epidermidis	Staphylococcus_epidermidis_unclassified
+16.29021		Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus	Streptococcus_mutans	Streptococcus_mutans_unclassified
+6.70485		Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia	Escherichia_coli	Escherichia_coli_unclassified
+6.518		Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter	Methanobrevibacter_smithii	Methanobrevibacter_smithii_unclassified
+5.59702		Bacteria	Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	Rhodobacter	Rhodobacter_sphaeroides	Rhodobacter_sphaeroides_unclassified
+0.9463		Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium	Clostridium_beijerinckii	Clostridium_beijerinckii_unclassified
+0.82072		Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus	Streptococcus_agalactiae	Streptococcus_agalactiae_unclassified
+0.81027		Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	Pseudomonas_aeruginosa	Pseudomonas_aeruginosa_unclassified
+0.36084		Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium	Propionibacterium_acnes	Propionibacterium_acnes_unclassified
+0.15178		Bacteria	Deinococcus_Thermus	Deinococci	Deinococcales	Deinococcaceae	Deinococcus	Deinococcus_radiodurans	GCF_000008565
+0.12046		Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter	Acinetobacter_baumannii	Acinetobacter_baumannii_unclassified
+0.07684		Bacteria	Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	Helicobacter	Helicobacter_pylori	Helicobacter_pylori_unclassified
+0.04347		Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria	Neisseria_meningitidis	Neisseria_meningitidis_unclassified
diff -r 3f52f2d65d41 -r fb2dc25a832d tool-data/metaphlan2_bowtie_db.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/metaphlan2_bowtie_db.loc.sample	Tue Apr 12 03:07:32 2016 -0400
@@ -0,0 +1,5 @@
+# Bowtie2 db have to be downloaded from https://bitbucket.org/biobakery/metaphlan2/src/5424bb911dfc/db_v20/?at=default (whole directory)
+#
+#Since MetaPhlAn comes bundled with 1 Bowtie2 database, you can use it
+#by downloading it as explained above and uncommenting the following lines.
+#bowtie_db_v20 Defaut BowTie2 database  $METAPHLAN2_DIR/db_v20/mpa_v20_m200
diff -r 3f52f2d65d41 -r fb2dc25a832d tool-data/metaphlan2_metadata.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/metaphlan2_metadata.loc.sample	Tue Apr 12 03:07:32 2016 -0400
@@ -0,0 +1,5 @@
+#Metadata have to be downloaded from https://bitbucket.org/biobakery/metaphlan2/raw/5424bb911dfcdb7212ea0949d4faeb6e69cfa61f/db_v20/mpa_v20_m200.pkl
+#
+#Since MetaPhlAn comes bundled with 1 metadata database, you can use it
+#by downloading it as explained above and uncommenting the following lines.
+#metadata_db_v20	Defaut MetaPhlAn2 metadata	$METAPHLAN2_DIR/db_v20/mpa_v20_m200.pkl
diff -r 3f52f2d65d41 -r fb2dc25a832d tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Apr 12 03:07:32 2016 -0400
@@ -0,0 +1,10 @@
+<tables>
+    <table name="metaphlan2_metadata" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/metaphlan2_metadata.loc" />
+    </table>
+    <table name="metaphlan2_bowtie_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/metaphlan2_bowtie_db.loc" />
+    </table>
+</tables>
diff -r 3f52f2d65d41 -r fb2dc25a832d tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Mar 31 05:45:29 2016 -0400
+++ b/tool_dependencies.xml	Tue Apr 12 03:07:32 2016 -0400
@@ -4,6 +4,6 @@
         <repository changeset_revision="f5582ac5ba3c" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="metaphlan2" version="2.2.0">
-        <repository changeset_revision="bbac0ef27bb2" name="package_metaphlan2_2_2_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="3cb6227f905e" name="package_metaphlan2_2_2_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>