diff presto_parselog.xml @ 0:488cd05be723 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/presto_parselog.xml	Wed May 30 15:35:52 2018 -0400
@@ -0,0 +1,46 @@
+<tool id="presto_parselog" name="pRESTO ParseLog" version="@PRESTO_VERSION@">
+    <description>Create tabular report from pRESTO log file</description>
+    
+    <macros>
+        <import>presto_macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements"/>
+    
+    <version_command>ParseLog.py --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        ParseLog.py 
+          -l '$log_file'
+          -f $fields
+          --outdir=.
+          --outname=tmp
+    ]]></command>
+
+    <inputs>
+        <param argument="-l" name="log_file" type="data" format="txt" label="pRESTO log file" help="Detailed log file generated from a pRESTO tool."/>
+        <param argument="-f" name="fields" type="text" label="Field(s)" help="Space-separated list of fields to extract.">
+            <expand macro="text-regex-validator"/>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="tsv" from_work_dir="tmp_table.tab"/>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param  name="log_file" value="presto_parselog_test_in.txt"/>
+            <param  name="fields" value="ID QUALITY"/>
+            <output name="output" file="presto_parselog_test_out.txt" sort="true"/>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+Creates tab-separated tabular reports from pRESTO detailed log files.
+
+See the `pRESTO online help <@PRESTO_URL_BASE@/ParseLog.html>`_ for more information.
+
+@HELP_NOTE@
+    ]]></help>
+    <expand macro="citations" />
+</tool>