diff macros.xml @ 1:3bdd8fa109b1 draft

"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"

--- a/macros.xml	Mon Jun 08 15:57:10 2020 -0400
+++ b/macros.xml	Fri Jun 12 15:08:23 2020 -0400
@@ -1,31 +1,83 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">3.1.3</token>
+    <token name="@TOOL_NAME@">ont_fast5_api:</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">ont-fast5-api</requirement>
+            <requirement type="package" version="1.10.5">hdf5</requirement>
         </requirements>
     </xml>
-	<xml name="citations">
-        <citations>
-            <citation type="bibtex">@online{ont_fast5_api,
-              author = {Oxford Nanopore Technologies },
-              title = {ont_fast5_api},
-              year = 2020,
-              url = {https://github.com/nanoporetech/ont_fast5_api},
-              urldate = {2020-06-01}    
-		    }</citation>
-        </citations>
+
+    <!-- command -->
+    <token name="@BATCHSIZE@"><![CDATA[
+--batch_size $batch_size
+    ]]></token>
+    <token name="@COMPRESSION@"><![CDATA[
+#if $compression != 'none'
+    --compression '$compression'
+#end if
+    ]]></token>
+    <token name="@INITIALIZE@"><![CDATA[
+mkdir -p './data' &&
+tar -xf '$input_path' -C './data' &&
+    ]]></token>
+    <token name="@INPUTPATH@"><![CDATA[
+--input_path './data'
+    ]]></token>
+    <token name="@SAVEPATH@"><![CDATA[
+--save_path './results'
+    ]]></token>
+    <token name="@TARBALL@"><![CDATA[
+&& find './results' -type f -name '*.fast5' | tar --transform 's/.*\///g' -cvf './results.fast5.tar' --files-from=/dev/stdin
+    ]]></token>
+    <token name="@THREADS@"><![CDATA[
+--threads \${GALAXY_SLOTS:-4}
+    ]]></token>
+
+    <!-- input -->
+    <xml name="input" token_argument="--input_path" token_label="multi">
+        <param argument="@ARGUMENT@" type="data" format="fast5.tar" label="Select @LABEL@ read input file"/>
     </xml>
-    <token name="@WID@"><![CDATA[
-ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.
+    <xml name="batch_size">
+        <param argument="--batch_size" type="integer" value="4000" min="1" label="Set batch size" help="Number of single reads to include in each multi read file"/>
+    </xml>
+    <xml name="compression">
+        <param argument="compression" type="select" label="Select output compression type">
+            <yield/>
+            <option value="vbz_legacy_v0">VBZ legacy v0</option>
+            <option value="gzip">GZIP</option>
+        </param>
+    </xml>
 
-- Concrete implementation of the FAST5 file schema using the generic h5py library
-- Plain-english-named methods to interact with and reflect the FAST5 file schema
-- Tools to convert between multi_read and single_read formats
-- Tools to compress/decompress raw data in files
+    <!-- output -->
+    <xml name="output">
+        <data name="out_results" format="fast5.tar" from_work_dir="results.fast5.tar" label="${tool.name} on ${on_string}: Results"/>
+    </xml>
+
+   <!-- help -->
+    <token name="@WID@"><![CDATA[
+*ont_fast5_api* is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.
+
+- concrete implementation of the FAST5 file schema using the generic h5py library
+- plain-english-named methods to interact with and reflect the FAST5 file schema
+- tools to convert between multi_read and single_read formats
+- tools to compress/decompress raw data in files
     ]]></token>
     <token name="@REFERENCES@"><![CDATA[
 More information are available on `github <https://github.com/nanoporetech/ont_fast5_api>`_.
     ]]></token>
-</macros>
\ No newline at end of file
+
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @online{ont_fast5_api,
+                author = {Oxford Nanopore Technologies },
+                title = {ont_fast5_api},
+                year = 2020,
+                url = {https://github.com/nanoporetech/ont_fast5_api},
+                urldate = {2020-06-01}
+            }</citation>
+        </citations>
+    </xml>
+</macros>