# HG changeset patch
# User artbio
# Date 1620174161 0
# Node ID 0e548765d2045b498194f2994b6fad9db90031cb

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"

diff -r 000000000000 -r 0e548765d204 tarfast5.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tarfast5.xml	Wed May 05 00:22:41 2021 +0000
@@ -0,0 +1,61 @@
+<tool id="tarfast5" name="tarfast5" version="0.3">
+  <description></description>
+  <requirements>
+        <requirement type="package" version="2.6">pigz</requirement>
+        <requirement type="package" version="1.34">tar</requirement>
+  </requirements>
+  <stdio>
+      <exit_code range="1:" level="fatal" description="Tool exception" />
+  </stdio>
+  <command detect_errors="exit_code"><![CDATA[
+        #for $file in $inputs:
+            ln -s $file ${file.element_identifier}.h5 &&
+        #end for
+            tar -I pigz -cvhf $compressed_output *.h5
+  ]]></command>
+ <inputs>
+    <param name="inputs" type="data" format="h5" label="fast5 sequence files" multiple="true" />
+ </inputs>
+
+ <outputs>
+    <data format="fast5.tar.gz" name="compressed_output" label="tar.gz archive of fast5" />
+</outputs>
+
+    <tests>
+        <test> <!-- 0 -->
+            <param name="inputs" value="F1.fast5.h5,F2.fast5.h5" ftype="h5" />
+            <output file="archive.tar.gz" name="compressed_output" compare="sim_size" delta="3000" />
+        </test>
+    </tests>
+<help>
+
+**What it does**
+
+Creates a tar.gz archive of fast5 (h5) sequences files
+
+.. class:: warningmark
+
+This tools follows a "map-reduce" procedure: multiple inputs, that can be arranged as a data collection,
+are compressed into a single tar.gz archive.
+ 
+
+
+**Output**
+
+A fast5.tar.gz archive
+
+</help>
+
+<citations>
+    <citation type="doi">10.1093/bioinformatics/btp352</citation>
+     <citation type="bibtex">@Book{,
+    title = {Lattice: Multivariate Data Visualization with R},
+    author = {Deepayan Sarkar},
+    publisher = {Springer},
+    address = {New York},
+    year = {2008},
+    note = {ISBN 978-0-387-75968-5},
+    url = {http://lmdvr.r-forge.r-project.org},
+  }</citation>
+</citations>
+</tool>
diff -r 000000000000 -r 0e548765d204 test-data/F1.fast5.h5
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diff -r 000000000000 -r 0e548765d204 test-data/F2.fast5.h5
Binary file test-data/F2.fast5.h5 has changed
diff -r 000000000000 -r 0e548765d204 test-data/archive.tar.gz
Binary file test-data/archive.tar.gz has changed