diff compress_fast5.xml @ 0:0fbeff566070 draft default tip

"planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/ont_fast5_api commit 9fb27995131a4106053eb85d687857d2cbd2a5c6"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compress_fast5.xml	Sat May 22 15:11:43 2021 +0000
@@ -0,0 +1,99 @@
+<?xml version="1.0"?>
+<tool id="ont_fast5_api_compress_fast5" name="@TOOL_NAME@ Compress" version="@TOOL_VERSION@+galaxy0" profile="18.01">
+    <description>multi read file(s)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <version_command><![CDATA[compress_fast5 -v]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+## initialize
+@INITIALIZE@
+
+## run
+compress_fast5
+--recursive
+## required
+@INPUTPATH@
+@SAVEPATH@
+--compression '$compression'
+## optional
+@THREADS@
+
+## create tarball
+@TARBALL@
+    ]]></command>
+    <inputs>
+        <expand macro="input"/>
+        <param argument="compression" type="select" label="Select output compression type">
+            <option value="gzip" selected="true">GZIP</option>
+            <option value="vbz_legacy_v0">VBZ legacy v0</option>
+            <option value="vbz">VBZ</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_results" format="fast5.tar" from_work_dir="results.fast5.tar" label="${tool.name} on ${on_string}: Results">
+            <change_format>
+                <when input="compression" value="gzip" format="fast5.tar.gz"/>
+                <when input="compression" value="vbz_legacy_v0" format="fast5.tar.bz2"/>
+                <when input="compression" value="vbz" format="fast5.tar.bz2"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <!-- #1 default -->
+        <test expect_num_outputs="1">
+            <param name="input_path" value="multi.fast5.tar"/>
+            <param name="compression" value="vbz"/>
+            <output name="out_results">
+                <assert_contents>
+                    <has_size value="40960"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #2 -->
+        <test expect_num_outputs="1">
+            <param name="input_path" value="multi.fast5.tar"/>
+            <param name="compression" value="vbz_legacy_v0"/>
+            <output name="out_results">
+                <assert_contents>
+                    <has_size value="40960"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #3 -->
+        <test expect_num_outputs="1">
+            <param name="input_path" value="multi.fast5.tar"/>
+            <param name="compression" value="gzip"/>
+            <output name="out_results">
+                <assert_contents>
+                    <has_size value="40960"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+*compress_fast5* copies and converts raw data between vbz and gzip compression formats.
+
+**Input**
+
+Multi read file(s) in FAST5 format that are stored in a flat TAR.
+
+**Output**
+
+Multi read FAST5 file(s) containing compressed reads that are stored in a flat TAR. Further detail of HDF5 data management strategies can be found `here <https://support.hdfgroup.org/HDF5/doc/Advanced/FileSpaceManagement/FileSpaceManagement.pdf>`_.
+
+.. class:: infomark
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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