# HG changeset patch
# User bebatut
# Date 1487753375 18000
# Node ID c941148c75c78d848177cec8ea40e487e21fd5e9
# Parent  83f06bee818c505c7529bac6240eb27dbe93ea84
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 9e93b527d3cc9023467b1b285b068dac21b0727b-dirty

diff -r 83f06bee818c -r c941148c75c7 README.rst
--- a/README.rst	Tue Feb 21 12:29:37 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-Galaxy wrappers for MetaPhlAn2
-==============================
-
-Galaxy should be able to automatically install the dependencies, i.e. the
-MetaPhlAn2 binaries.
-
-After installation, you must tell Galaxy about the defaut database with
-clade-specific marker genes, and where to find it:
-
-* Put the ``metaphlan2_db.loc`` file in the ``tool-data/`` folder, after uncommenting last line
-* Download whole MetaPhlan2 source code: https://bitbucket.org/biobakery/metaphlan2/get/2.5.0.zip
-* Unzip it
-* Move ``db_v20`` folder into ``dependency_dir/metaphlan2/2.5.0/bebatut/package_metaphlan2_2_5_0/...`` folder
diff -r 83f06bee818c -r c941148c75c7 extract_markers.xml
--- a/extract_markers.xml	Tue Feb 21 12:29:37 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-<tool id="metaphlan2_extract_markers" name="Format MetaPhlAn2" version="@WRAPPER_VERSION@.0">
-
-    <description>output for Krona</description>
-
-    <macros>
-        <import>metaphlan2_macros.xml</import>
-    </macros>
-
-    <expand macro="requirements"/>
-    <expand macro="stdio"/>
-
-    <version_command>extract_markers.py -v</version_command>
-
-    <command>
-<![CDATA[
-        extract_markers.py
-            --mpa_pkl MPA_PKL
-            --ifn_markers IFN_MARKERS
-            --clade CLADE
-            --ofn_markers OFN_MARKERS
-]]>
-    </command>
-
-    <inputs>
-        <param name="input_file" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)" help="(--profile)"/>
-    </inputs>
-
-    <outputs>
-        <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Formatted file for Krona" />
-    </outputs>
-
-    <tests>
-        <test>
-            <param name="input_file" value="community_profile.tabular"/>
-            <output name="krona" file="formatted_to_krona.tabular"/>
-        </test>
-    </tests>
-
-    <help><![CDATA[
-
-**What it does**
-
-MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
-
-This tool formats MetaPhlAn2 output to be ready for Krona.
-
-    ]]></help>
-
-    <expand macro="citations"/>
-</tool>
diff -r 83f06bee818c -r c941148c75c7 metaphlan2.xml
--- a/metaphlan2.xml	Tue Feb 21 12:29:37 2017 -0500
+++ b/metaphlan2.xml	Wed Feb 22 03:49:35 2017 -0500
@@ -43,10 +43,11 @@
             --bowtie2_exe `which bowtie2`
 
             #if $db.db_selector == "cached"
-                #set $table = dict([(_[0], _[2]) for _ in $db.cached_db.input.options.tool_data_table.data])
+                #set $paths = dict([(_[0], _[3]) for _ in $db.cached_db.input.options.tool_data_table.data])
                 #set $db_choice = $db.cached_db.value
-                --bowtie2db '$table[$db_choice]'
-                --mpa_pkl $table[$db_choice]".pkl"
+                #set $metadata = `ls $paths[$db_choice]/*.pkl`
+                --bowtie2db $metadata[:-4]
+                --mpa_pkl '$metadata'
             #else
                 --bowtie2db 'ref_db/ref_db'
                 --mpa_pkl 'ref_db/metadata.pkl'
diff -r 83f06bee818c -r c941148c75c7 metaphlan_hclust_heatmap.xml
--- a/metaphlan_hclust_heatmap.xml	Tue Feb 21 12:29:37 2017 -0500
+++ b/metaphlan_hclust_heatmap.xml	Wed Feb 22 03:49:35 2017 -0500
@@ -222,7 +222,7 @@
             <param name="font_size" value="7"/>
             <param name="clust_line_w" value="1"/>
             <param name="c" value="jet"/>
-            <output name="out_png" file="heatmap.png" lines_diff='5'/>
+            <output name="out_png" file="heatmap.png" ftype="png" compare="sim_size"/>
         </test>
         <test>
             <param name="in" value="merged_community_profile.tabular"/>
@@ -239,7 +239,7 @@
             <param name="font_size" value="7"/>
             <param name="clust_line_w" value="1"/>
             <param name="c" value="pink"/>
-            <output name="out_pdf" md5="35702e08d994cd64371cdce3e025dc5a"/>
+            <output name="out_pdf" file="heatmap.pdf" compare="sim_size"/>
         </test>
         <test>
             <param name="in" value="merged_community_profile.tabular"/>
@@ -256,7 +256,7 @@
             <param name="font_size" value="7"/>
             <param name="clust_line_w" value="1"/>
             <param name="c" value="pink"/>
-            <output name="out_svg" md5="844799aca7af03db2c2f6222b873c8cf"/>
+            <output name="out_svg" file="heatmap.svg" ftype="svg" compare="sim_size"/>
         </test>
     </tests>
 
diff -r 83f06bee818c -r c941148c75c7 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Tue Feb 21 12:29:37 2017 -0500
+++ b/tool_data_table_conf.xml.sample	Wed Feb 22 03:49:35 2017 -0500
@@ -1,6 +1,6 @@
 <tables>
     <table name="metaphlan2_database" comment_char="#">
-        <columns>value, name, path</columns>
+        <columns>value, name, dbkey, path</columns>
         <file path="tool-data/metaphlan2_database.loc" />
     </table>
 </tables>
diff -r 83f06bee818c -r c941148c75c7 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Feb 21 12:29:37 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="numpy" version="1.9">
-        <repository changeset_revision="5f2b261ffc5b" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bowtie2" version="2.2.5">
-        <repository changeset_revision="f5582ac5ba3c" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="metaphlan2" version="2.5.0">
-        <repository changeset_revision="33e53932c13a" name="package_metaphlan2_2_5_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>