Mercurial > repos > iuc > khmer_abundance_distribution

diff abundance-dist.xml @ 0:c07433531fd3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
author iuc
date Wed, 11 Nov 2015 09:46:38 -0500
parents
children be929aa4e152
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abundance-dist.xml	Wed Nov 11 09:46:38 2015 -0500
@@ -0,0 +1,69 @@
+<tool id="khmer_abundance_distribution" name="Abundance Distribution" version="@WRAPPER_VERSION@.0">
+    <description>
+        Calculate abundance distribution of the k-mers in a given sequence file using a pre-made k-mer countgraph
+    </description>
+    <macros>
+        <token name="@BINARY@">abundance-dist.py</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version" />
+    <command><![CDATA[
+set -xu &&
+mkdir output && cd output &&
+@BINARY@
+--squash
+${zero}
+${bigcount}
+${input_countgraph_filename}
+${input_sequence_filename}
+${output_histogram_filename}
+]]>
+    </command>
+    <inputs>
+        <expand macro="input_countgraph_filename" />
+        <expand macro="input_sequence_filename" />
+        <expand macro="input_zero" />
+        <expand macro="input_bigcount" />
+    </inputs>
+    <outputs>
+        <expand macro="abundance-histogram-output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_sequence_filename" value="test-abund-read-2.fa" />
+            <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />
+            <param name="zero" value="false" />
+            <output name="output_histogram_filename">
+                <assert_contents>
+                    <has_text text="1,96,96,0.98" />
+                    <has_text text="1001,2,98,1.0" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_sequence_filename" value="test-abund-read-2.fa" />
+            <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />
+            <param name="zero" value="false" />
+            <param name="bigcount" value="false" />
+            <output name="output_histogram_filename">
+                <assert_contents>
+                    <has_text text="1,96,96,0.98" />
+                    <has_text text="255,2,98,1.0" />
+                    </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Calculate abundance distribution of the k-mers in the sequence file using a
+pre-made k-mer countgraph.
+
+@HELP_FOOTER@
+]]>
+    </help>
+    <citations>
+        <expand macro="software-citation" />
+        <expand macro="counting-citation" />
+    </citations>
+</tool>