diff abundance-dist-single.xml @ 0:47cea67b74ea draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abundance-dist-single.xml	Wed Nov 11 09:47:17 2015 -0500
@@ -0,0 +1,91 @@
+<tool id="khmer_abundance_distribution_single" name="Abundance Distribution (all-in-one)" version="@WRAPPER_VERSION@.0">
+    <description>
+        Calculate abundance distribution of the k-mers in a given sequence file
+    </description>
+    <macros>
+        <token name="@BINARY@">abundance-dist-single.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@
+@TABLEPARAMS@
+${zero}
+${bigcount}
+#if $save_countgraph
+    --savegraph=${optional_output_countgraph}
+#end if
+--squash
+@THREADS@
+${input_sequence_filename}
+${output_histogram_filename}
+
+]]>
+    </command>
+    <inputs>
+        <expand macro="input_sequence_filename" />
+        <param name="save_countgraph" type="boolean" label="Save the k-mer countgraph to a file"
+            help="(--savegraph)" />
+        <expand macro="input_zero" />
+        <expand macro="input_bigcount" />
+        <expand macro="tableinputs" />
+    </inputs>
+    <outputs>
+        <data name="optional_output_countgraph" format="oxlicg" label="${tool.name} k-mer countgraph">
+            <filter>save_countgraph == True</filter>
+        </data>
+        <expand macro="abundance-histogram-output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_sequence_filename" value="test-abund-read-2.fa" />
+            <param name="type" value="specific" />
+            <param name="tablesize_specific" value="1e7" />
+            <param name="n_tables" value="2" />
+            <param name="ksize" value="17" />
+            <param name="no_zero" value="false" />
+            <output name="output_histogram_filename" ftpye="txt">
+                <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="type" value="specific" />
+            <param name="tablesize_specific" value="1e7" />
+            <param name="n_tables" value="2" />
+            <param name="ksize" value="17" />
+            <param name="no_zero" value="false" />
+            <param name="bigcount" value="false" />
+            <output name="output_histogram_filename" ftype="txt">
+                <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 the abundance distribution of k-mers from a single sequence file.
+
+Note that with `-b` this script is constant memory; in exchange,
+k-mer counts will stop at 255. The memory usage of this script with
+`-b` will be about 1.15x the product of the `-x` and
+`-N` numbers.
+
+
+@HELP_FOOTER@
+]]>
+    </help>
+    <citations>
+        <expand macro="software-citation" />
+        <expand macro="counting-citation" />
+    </citations>
+</tool>