Mercurial > repos > iuc > khmer_extract_partitions

diff extract-partitions.xml @ 0:d5a18dd63529 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 09:47:38 -0500
parents
children 2c763fb18010
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract-partitions.xml	Wed Nov 11 09:47:38 2015 -0500
@@ -0,0 +1,57 @@
+<tool id="khmer_extract_partitions" name="Extract partitions" version="@WRAPPER_VERSION@.0">
+    <description>Separate sequences that are annotated with partitions into grouped files</description>
+    <macros>
+        <token name="@BINARY@">extract-partitions.py</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version" />
+    <command><![CDATA[
+mkdir -p output &&
+cd output &&
+@BINARY@
+--max-size $max_size
+--min-partition-size $min_partition_size
+$output_unassigned
+output
+#for input in $inputs
+    $input
+#end for
+]]>
+    </command>
+    <inputs>
+        <expand macro="input_sequences_filenames" />
+        <param name="max_size" type="integer" label="Max group size" value="1000000"
+            help="No more than this many number of sequences will be stored in each output (--max-size/-X)"/>
+        <param name="min_partition_size" type="integer" label="Min partition size" value="5"
+            help="The minimum partition size worth keeping (--min-partition-size/-m)" />
+        <param name="output_unassigned" type="boolean" checked="false" truevalue="--output-unassigned" falsevalue=""
+            label="Output unassigned sequences" help="(--output-unassigned/-U)" />
+    </inputs>
+    <outputs>
+        <data name="distribution" format="txt" from_work_dir="output.dist" label="Partition size distribution from ${tool.name}" />
+        <collection name="groups-of-partitions" type="list">
+            <discover_datasets pattern="__name__" directory="output" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" value="random-20-a.fa.part"/>
+            <output_collection name="groups-of-partitions">
+                <element name="output.group0000.fa" file="random-20-a.part.extract.fa" />
+            </output_collection>
+        </test>
+
+    </tests>
+    <help><![CDATA[
+Separate sequences that are annotated with partitions into grouped files.
+
+@HELP_FOOTER@
+]]>
+    </help>
+    <citations>
+        <expand macro="software-citation" />
+        <expand macro="graph-citation" />
+    </citations>
+</tool>