Mercurial > repos > iuc > biom_subset_table

diff biom_subset_table.xml @ 0:806ff6f90364 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 12:39:28 -0400
parents
children 9d84e99a4253
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/biom_subset_table.xml	Wed Sep 11 12:39:28 2019 -0400
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+<tool id="biom_subset_table" name="Subset" version="@VERSION@.1">
+    <description>a BIOM table</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code">
+        <![CDATA[
+            biom subset-table
+              --input-json-fp '$input_json_fp'
+              --output-fp '$output_fp'
+              --axis '$axis'
+              --ids '$ids'
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_json_fp" argument="--input-json-fp" type="data" format="biom1" label="BIOM table to subset" />
+        <param argument="--axis" type="select" label="The axis to subset over">
+            <option value="sample" selected="True">Sample</option>
+            <option value="observation">Observation</option>
+        </param>
+        <param argument="--ids" type="data" format="text,tabular" label="file containing a single column of IDs to retain" />
+    </inputs>
+    <outputs>
+        <data format="biom1" name="output_fp"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_json_fp" value="input_abundance_1.biom1" />
+            <param name="axis" value="sample" />
+            <param name="ids" value="sample_subsetting" />
+            <output name="output_fp" file="subset_samples.biom" ftype="biom1" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="input_json_fp" value="input_abundance_1.biom1" />
+            <param name="axis" value="observation" />
+            <param name="ids" value="observation_subsetting" />
+            <output name="output_fp" file="subset_observations.biom" ftype="biom1" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Subset a BIOM table, over either observations or samples, without fully parsing it. This command is intended to assist in working with very large tables when tight on memory, or as a lightweight way to subset a full table. Currently, it is possible to produce tables with rows or columns (observations or samples) that are fully zeroed.
+    ]]></help>
+    <expand macro="citations" />
+</tool>