Mercurial > repos > iuc > biom_summarize_table

diff biom_summarize_table.xml @ 0:8f4407e9891c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
author iuc
date Wed, 11 Sep 2019 12:39:57 -0400
parents
children 2cc55cbcb4a3
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/biom_summarize_table.xml	Wed Sep 11 12:39:57 2019 -0400
@@ -0,0 +1,43 @@
+<tool id="biom_summarize_table" name="Summarize sample or observation data" version="@VERSION@.1">
+    <description>in a BIOM table</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code">
+        <![CDATA[
+            biom summarize-table
+              --input-fp '$input_fp'
+              --output-fp '$output_fp'
+              $qualitative
+              $observations
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="Input BIOM table" />
+        <param argument="--qualitative" type="boolean" checked="True" truevalue="--qualitative" falsevalue="" label="Present counts as number of unique observation ids per sample, rather than counts of observations per sample" />
+        <param argument="--observations" type="boolean" checked="True" truevalue="--observations" falsevalue="" label="Summarize over observations" />
+    </inputs>
+    <outputs>
+        <data format="text" name="output_fp"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_fp" value="input_abundance_1.biom1" />
+            <param name="qualitative" value="" />
+            <param name="observations" value="" />
+            <output name="output_fp" value="summarize" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="input_fp" value="input_abundance_1.biom1" />
+            <param name="qualitative" value="--qualitative" />
+            <param name="observations" value="--observations" />
+            <output name="output_fp" value="summarize_qualitative_observations" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Provides details on the observation counts per sample, including summary statistics, as well as metadata categories associated with samples and observations.
+    ]]></help>
+    <expand macro="citations" />
+</tool>