changeset 1:9be4beda6482 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"

--- a/metaphlan2.xml	Sat Mar 04 12:23:45 2017 -0500
+++ b/metaphlan2.xml	Fri Mar 19 09:38:42 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.0">
+<tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.1">
 
     <description>to profile the composition of microbial communities</description>
 
@@ -10,68 +10,68 @@
         <requirement type="package" version="2.3.0">bowtie2</requirement>
         <requirement type="package" version="2.7.10">python</requirement>
     </expand>
-    
+
     <expand macro="stdio"/>
 
-    <version_command>
-<![CDATA[
-metaphlan2.py -v
-]]>
-    </version_command>
+    <version_command>metaphlan2.py -v</version_command>
 
-    <command>
-<![CDATA[
-        #if $db.db_selector == "history"
-            mkdir ref_db
-            &&
-            bowtie2-build '$db.bowtie2db' 'ref_db/ref_db'
-            &&
-            python '$__tool_directory__/transform_json_to_pkl.py'
-                --json_input '$db.mpa_pkl'
-                --pkl_output 'ref_db/metadata.pkl'
-            &&
-        #end if
+    <command><![CDATA[
+#if $db.db_selector == "history"
+    mkdir ref_db
+    &&
+    bowtie2-build '$db.bowtie2db' 'ref_db/ref_db'
+    &&
+    python '$__tool_directory__/transform_json_to_pkl.py'
+        --json_input '$db.mpa_pkl'
+        --pkl_output 'ref_db/metadata.pkl'
+    &&
+#end if
 
-        metaphlan2.py
-            '$input_file'
-            -o '$output_file'
-            --input_type '${input_file.datatype.file_ext}'
-            --bowtie2_exe `which bowtie2`
+#if $input_file.datatype.file_ext.startswith("fastq")
+    #set ext='fastq'
+#else
+    #set ext=$input_file.datatype.file_ext
+#end if
+
+metaphlan2.py
+    '$input_file'
+    -o '$output_file'
+    --input_type $ext
+    --bowtie2_exe `which bowtie2`
 
-            #if $db.db_selector == "cached"
-                #set $path = $db.cached_db.fields.path
-                #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'
-            #end if
+    #if $db.db_selector == "cached"
+        #set $path = $db.cached_db.fields.path
+        #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'
+    #end if
 
-            --no_map
+    --no_map
 
-            -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.tax_lev'
-            #else if $analysis_type.analysis_type_select == "marker_ab_table"
-                --nreads '$analysis_type.nreads'
-            #else if $analysis_type.analysis_type_select == "marker_pres_table"
-                --pres_th '$analysis_type.pres_th'
-            #end if
+    -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.tax_lev'
+    #else if $analysis_type.analysis_type_select == "marker_ab_table"
+        --nreads '$analysis_type.nreads'
+    #else if $analysis_type.analysis_type_select == "marker_pres_table"
+        --pres_th '$analysis_type.pres_th'
+    #end if
 
-            --min_cu_len '$min_cu_len'
-            --min_alignment_len '$min_alignment_len'
+    --min_cu_len '$min_cu_len'
+    --min_alignment_len '$min_alignment_len'
 
-            $ignore_viruses
-            $ignore_eukaryotes
-            $ignore_bacteria
-            $ignore_archaea
+    $ignore_viruses
+    $ignore_eukaryotes
+    $ignore_bacteria
+    $ignore_archaea
 
-            --stat_q '$stat_q'
-            -s '$sam_output_file'
-            --biom '$biom_output_file'
-]]>
-    </command>
+    --stat_q '$stat_q'
+    -s '$sam_output_file'
+    --biom '$biom_output_file'
+    ]]></command>
 
     <inputs>
         <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file"/>
@@ -126,9 +126,9 @@
     </inputs>
 
     <outputs>
-        <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" />
-        <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" />
-        <data format="biom" name="biom_output_file" label="${tool.name} on ${on_string}: BIOM file" />
+        <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Community profile" />
+        <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file" />
+        <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />
     </outputs>
 
     <tests>

--- a/repository_dependencies.xml	Sat Mar 04 12:23:45 2017 -0500
+++ b/repository_dependencies.xml	Fri Mar 19 09:38:42 2021 +0000
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <repositories description="This requires the MetaPhlAn2 data manager definition to install all required databases.">
-    <repository changeset_revision="9c4ad82be5bd" name="data_manager_metaphlan2_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-</repositories>
+    <repository name="data_manager_metaphlan2_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="83f07f40b200"/>
+</repositories>
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