# HG changeset patch
# User bebatut
# Date 1488472115 18000
# Node ID 34114d4670fe5813deb8c0c8cf967f708e511b30
# Parent  1767fd901e8c5ec30173588f1c1e4564331e7caf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'cf8373aeed58964f1d139a23cd1ec4698683c60e\n'-dirty

diff -r 1767fd901e8c -r 34114d4670fe metaphlan2.xml
--- a/metaphlan2.xml	Wed Mar 01 11:07:43 2017 -0500
+++ b/metaphlan2.xml	Thu Mar 02 11:28:35 2017 -0500
@@ -40,8 +40,9 @@
 
             #if $db.db_selector == "cached"
                 #set $path = $db.cached_db.fields.path
-                --bowtie2db `ls $path/*.pkl | sed 's/\(.*\)\..*/\1/'`
-                --mpa_pkl `ls $path/*.pkl`
+                #set $value = $db.cached_db.fields.value
+                --bowtie2db $path/$value
+                --mpa_pkl $path/$value'.pkl'
             #else
                 --bowtie2db 'ref_db/ref_db'
                 --mpa_pkl 'ref_db/metadata.pkl'
@@ -51,7 +52,7 @@
 
             -t '$analysis_type.analysis_type_select'
             #if $analysis_type.analysis_type_select == "rel_ab" or $analysis_type.analysis_type_select == "rel_ab_w_read_stats"
-                --tax_lev '$analysis_type.taxonomic_level'
+                --tax_lev '$analysis_type.tax_lev'
             #else if $analysis_type.analysis_type_select == "marker_ab_table"
                 --nreads '$analysis_type.nreads'
             #else if $analysis_type.analysis_type_select == "marker_pres_table"
@@ -91,37 +92,19 @@
         </conditional>
         <conditional name="analysis_type">
             <param name="analysis_type_select" type="select" label="Type of analysis to perform" argument="-t">
-              <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
-              <option value="rel_ab_w_read_stats">Profiling a metagenomes in terms of relative abundances and estimate the number of reads comming from each clade</option>
-              <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
-              <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
-              <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option>
-              <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option>
-              <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
+                <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
+                <option value="rel_ab_w_read_stats">Profiling a metagenomes in terms of relative abundances and estimate the number of reads comming from each clade</option>
+                <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
+                <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
+                <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option>
+                <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option>
+                <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
             </param>
             <when value="rel_ab">
-              <param argument="--taxonomic_level" type="select" label="Taxonomic level for the relative abundance output">
-                <option value="a" selected="true">All taxonomic levels</option>
-                <option value="k">Kingdoms (Bacteria and Archaea) only</option>
-                <option value="p">Phyla only</option>
-                <option value="c">Classes only</option>
-                <option value="o">Orders only</option>
-                <option value="f">Families only</option>
-                <option value="g">Genera only</option>
-                <option value="s">Species only</option>
-              </param>
+                <expand macro="tax_lev"/>
             </when>
             <when value="rel_ab_w_read_stats">
-              <param argument="--taxonomic_level" type="select" label="Taxonomic level for the relative abundance output">
-                <option value="a" selected="true">All taxonomic levels</option>
-                <option value="k">Kingdoms (Bacteria and Archaea) only</option>
-                <option value="p">Phyla only</option>
-                <option value="c">Classes only</option>
-                <option value="o">Orders only</option>
-                <option value="f">Families only</option>
-                <option value="g">Genera only</option>
-                <option value="s">Species only</option>
-              </param>
+                <expand macro="tax_lev"/>
             </when>
             <when value="reads_map"/>
             <when value="clade_profiles"/>
diff -r 1767fd901e8c -r 34114d4670fe metaphlan2_macros.xml
--- a/metaphlan2_macros.xml	Wed Mar 01 11:07:43 2017 -0500
+++ b/metaphlan2_macros.xml	Thu Mar 02 11:28:35 2017 -0500
@@ -25,4 +25,16 @@
           <citation type="doi">10.1038/nmeth.3589</citation>
       </citations>
     </xml>
+    <xml name="tax_lev">
+      <param argument="--tax_lev" type="select" label="Taxonomic level for the relative abundance output">
+        <option value="a" selected="true">All taxonomic levels</option>
+        <option value="k">Kingdoms (Bacteria and Archaea) only</option>
+        <option value="p">Phyla only</option>
+        <option value="c">Classes only</option>
+        <option value="o">Orders only</option>
+        <option value="f">Families only</option>
+        <option value="g">Genera only</option>
+        <option value="s">Species only</option>
+      </param>
+    </xml>
 </macros>
diff -r 1767fd901e8c -r 34114d4670fe repository_dependencies.xml
--- a/repository_dependencies.xml	Wed Mar 01 11:07:43 2017 -0500
+++ b/repository_dependencies.xml	Thu Mar 02 11:28:35 2017 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the MetaPhlAn2 data manager definition to install all required databases.">
-    <repository changeset_revision="8602983cb86f" name="data_manager_metaphlan2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="bf858d6f7365" name="data_manager_metaphlan2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>