diff humann_join_tables.xml @ 0:4c8c07939fcf draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann_join_tables.xml	Mon Feb 13 16:19:22 2023 +0000
@@ -0,0 +1,46 @@
+<tool id="humann_join_tables" name="Join (merge)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
+    <description>gene, pathway, or taxonomy HUMAnN/MetaPhlAn tables into a single table</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+mkdir tmp_dir
+&&
+#for $input in $inputs
+ln -s '$input' 'tmp_dir/${re.sub('[^\w\-_.]', '_', input.element_identifier)}' &&
+#end for
+humann_join_tables
+    -i 'tmp_dir'
+    -o '$output'
+    ]]></command>
+    <inputs>
+        <param name="inputs" type="data" format="tsv,tabular" multiple="true" label="Gene/pathway table"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="inputs" value="demo_pathabundance.tsv,demo_pathcoverage.tsv"/>
+            <output name="output" ftype="tabular" value="demo_joined_pathabundance_pathcoverage.tsv">
+                <assert_contents>
+                    <has_text text="humann_Abundance" />
+                    <has_text text="humann_Coverage" />
+                    <has_text text="UNINTEGRATED|unclassified" />
+                    <has_text text="PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+This tool joins (merges) multiple single-sample output files into a single table with multiple samples.
+It can also be used to join multiple multi-sample output files into a single table.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>