changeset 32:c941148c75c7 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 9e93b527d3cc9023467b1b285b068dac21b0727b-dirty

--- 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

--- 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>

--- 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'

--- 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>
 

--- 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>

--- 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>