diff alpha_diversity.xml @ 0:e400e5ef0e7c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alpha_diversity.xml	Fri Jan 13 13:21:35 2023 +0000
@@ -0,0 +1,99 @@
+<tool id="krakentools_alpha_diversity" name="Krakentools: Calculates alpha diversity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>from the Bracken abundance estimation file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements">
+        <requirement type="package" version="1.9.3">scipy</requirement>
+    </expand>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+alpha_diversity.py 
+    --filename '$filename'
+    --alpha '$alpha'
+    > '$output'
+    ]]></command>
+    <inputs>
+        <param argument="--filename" type="data" format="tabular" label="Abundance file" help="The file can be created by Bracken"/>
+        <param argument="--alpha" type="select" label="Specify alpha diversity type">
+            <option value="Sh" selected="true">Shannon's alpha diversity</option>
+            <option value="BP">Berger-Parker's alpha</option>
+            <option value="Si">Simpson's diversity</option>
+            <option value="ISi">Inverse Simpson's diversity</option>
+            <option value="F">Fisher's index</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="filename" value="bracken_abundance.tabular"/>
+            <param name="alpha" value="Sh"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text text="Shannon's diversity: 4.194127607417342"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="filename" value="bracken_abundance.tabular"/>
+            <param name="alpha" value="BP"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text text="Berger-parker's diversity: 0.05525121757950085"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="filename" value="bracken_abundance.tabular"/>
+            <param name="alpha" value="Si"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text text="Simpson's diversity: 0.9805668888241948"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="filename" value="bracken_abundance.tabular"/>
+            <param name="alpha" value="ISi"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text text="Simpson's Reciprocal Index: 51.45856424909617"/>
+                </assert_contents>
+            </output>              
+        </test>
+        <test>
+            <param name="filename" value="bracken_abundance.tabular"/>
+            <param name="alpha" value="F"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text text="Fisher's index: 1688.9352909860668"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs. These scripts are designed to help Kraken users with downstream analysis of Kraken results. This program calculates alpha diversity, from the Bracken abundance estimation file. User must specify Bracken output file, and type of alpha diversity to be calculated. Specific options are specified below.
+
+Input
+------
+Bracken abundance estimation file.
+
+Input Bracken file must be in standard Bracken output file format and must be run specifically for Abundance Estimation. Example format:
+    name                     tax_id tax_lvl kraken... added... new...  fraction...
+    Homo sapiens             9606   S       ...        ....    999000  0.999000
+    Streptococcus pyogenes   1314   S       ...        ....    10      0.000001
+    Streptococcus agalactiae 1311   S       ...        ....    5       0.000000
+    Streptococcus pneumoniae 1313   S       ...        ....    3       0.000000
+    Bordetella pertussis     520    S       ...        ....    20      0.000002
+
+Output
+---------
+Alpha diversity with the specified type.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>