diff render_datatable.xml @ 0:d4690e65afcd draft

Uploaded
author bcclaywell
date Thu, 26 Feb 2015 18:16:36 -0500
parents
children 3c50a937d7c1
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/render_datatable.xml	Thu Feb 26 18:16:36 2015 -0500
@@ -0,0 +1,63 @@
+<tool id="PHYLO_render_datatable" name="Render CSV file" version="1.1.0">
+  <description>as an interactive HTML table</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <command interpreter="bash">
+    render_datatable-wrapper.sh $config
+  </command>
+  <stdio>
+    <expand macro="basic_errors"/>
+  </stdio>
+  <inputs>
+    <param name="input" type="data" format="csv" label="CSV file"/>
+  </inputs>
+  <outputs>
+    <data format="html" name="output" label="Generated table"/>
+  </outputs>
+  <configfiles>
+    <configfile name="config">
+INPUT="${input}"
+
+OUTPUT="${output}"
+OUTPUT_DIR="${output.files_path}"
+    </configfile>
+  </configfiles>
+  <!-- The contents of the help tag is parsed as reStructuredText. Please see
+       help-template.rst for examples of commonly-used sections in other Galaxy
+       tools. -->
+  <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool reformats a CSV file, like this::
+
+    "seqname","accession","tax_id","species_name","is_type"
+    "FM872653","FM872653","308994","Dialister propionicifaciens",0.0
+    "AY331416","AY331416","239137","Candidate Division TM7 oral",0.0
+    "DQ666092","DQ666092","95818_1","Candidate Division TM7 vaginal",0.0
+    "S002223913","GQ900631","186802_3","bacterium BVAB3-Strain 1",0.0
+    ...
+
+into an interactive HTML table.
+
+[placeholder]
+
++-------------+-----------+----------+---------------------------------------+----------+
+|  seqname    | accession | tax_id   | species_name                          | is_type  |
++=============+===========+==========+=======================================+==========+
+|  FM872653   | FM872653  | 308994   | Dialister propionicifaciens           | 0.0      |
++-------------+-----------+----------+---------------------------------------+----------+
+|  AY331416   | AY331416  | 239137   | Candidate Division TM7 oral           | 0.0      |
++-------------+-----------+----------+---------------------------------------+----------+
+|  DQ666092   | DQ666092  | 95818_1  | Candidate Division TM7 vaginal        | 0.0      |
++-------------+-----------+----------+---------------------------------------+----------+
+|  S002223913 | GQ900631  | 186802_3 | bacterium BVAB3-Strain 1              | 0.0      |
++-------------+-----------+----------+---------------------------------------+----------+
+
+...
+
+  </help>
+</tool>