diff humann2_join_tables.xml @ 0:3d6f37e7e3a8 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_join_tables.xml	Thu May 26 10:20:59 2016 -0400
@@ -0,0 +1,58 @@
+<tool id="humann2_join_tables" name="Join" version="0.6.1">
+    <description>HUMAnN2 generated tables</description>
+
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <version_command>
+<![CDATA[
+    humann2_join_tables --version
+]]>
+    </version_command>
+
+    <command><![CDATA[
+        `mkdir tmp_dir`
+
+        && 
+
+        #for $table in $input_tables
+            `cp $table.input_table tmp_dir`
+        #end for
+
+        && 
+        humann2_join_tables
+            -i "tmp_dir"
+            -o $joined_table           
+    ]]></command>
+
+    <inputs>
+        <repeat name="input_tables" title="Gene/pathway tables to join">
+            <param name="input_table" type="data" format="tsv,tabular" multiple="true" label="Gene/pathway table" help=""/>
+        </repeat>
+    </inputs>
+
+    <outputs>
+        <data format="tsv" name="joined_table" label="${tool.name} on ${on_string}: Joined table" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_tables_0|input_table" value="expected_pathway_coverage.tsv"/>
+            <param name="input_tables_1|input_table" value="expected_pathway_abundance.tsv"/>
+            <output name="joined_table" file="joined_pathway_coverage_abundance.tsv"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
+
+Join HUMAnN2 tables is a tool to join gene or pathway tables of multiple samples into a single table.
+    ]]></help>
+
+    <expand macro="citations"/>
+</tool>
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