diff hicup_deduplicator.xml @ 0:d515a0639f8e draft

planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicup_deduplicator.xml	Thu Mar 09 09:30:33 2017 -0500
@@ -0,0 +1,39 @@
+<tool id="hicup_deduplicator" name="Hicup Deduplicator" version="0.1.0">
+    <description>removes duplicated di-tags (retaining one copy of each) from the data set.</description>
+    <macros>
+        <import>hicup_macros.xml</import>
+    </macros>
+    <expand macro="requirements_hicup" />
+    <expand macro="stdio" />
+
+    <command><![CDATA[
+        hicup_deduplicator --quiet '$input_file'
+        && mv *.dedup.* dataset.dedup_result
+        && mv hicup_deduplicator_summary*.txt hicup_deduplicator_summary.txt
+        && mv *deduplicator_cis_trans_piechart.svg deduplicator_cis_trans_piechart.svg
+        && mv *deduplicator_uniques_barchart.svg deduplicator_uniques_barchart.svg
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="bam,sam" label="Input file(s)" help="Input files in bam or sam format."/>
+    </inputs>
+    <outputs>
+       <data name="dedup_result" format="bam,sam" label="Deduplicator Result" from_work_dir="dataset.dedup_result" />
+       <expand macro="deduplicator_output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="dataset.filt.sam" ftype="sam"/>
+            <output name="dataset_hicup" file="dataset.hicup.sam" lines_diff="5" />
+            <output name="cis_trans_piechart" file="deduplicator_cis_trans_piechart.svg" ftype="svg" lines_diff="1000"/>
+            <output name="uniques_barchart" file="deduplicator_uniques_barchart.svg" ftype="svg" lines_diff="1000"/>
+            <output name="hicup_deduplicator_summary" file="hicup_deduplicator_summary.txt" lines_diff="2"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+    For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
+
+    To get more information about the deduplicator visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Deduplicator
+    ]]></help>
+    <expand macro="citation_hicup" />
+</tool>
\ No newline at end of file