changeset 4:04ec82208544 draft default tip

Uploaded

--- a/macros.xml	Thu Mar 19 17:58:54 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-<macros>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="0.67.5">circos</requirement>
-            <requirement type="package" version="0.20">circostools</requirement>
-            <yield/>
-        </requirements>
-    </xml>
-    <token name="@WRAPPER_VERSION@">0.67.5</token>
-    <xml name="stdio">
-        <stdio>
-            <!-- Anything other than zero is an error -->
-            <exit_code range="1:" />
-            <exit_code range=":-1" />
-            <!-- In case the return code has not been set propery check stderr too -->
-            <regex match="Error:" />
-            <regex match="Exception:" />
-        </stdio>
-    </xml>
-
-
-    <xml name="citations">
-        <citations>
-            <citation type="doi">10.1101/gr.092759.109</citation>
-            <yield />
-        </citations>
-    </xml>
-</macros>

--- a/simpletable.xml	Thu Mar 19 17:58:54 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-<tool id="circos_simpletable" name="Simple Table Plotter" version="@WRAPPER_VERSION@.0">
-    <description></description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <command>
-<![CDATA[
-cat $input |
-    perl \${CIRCOSTOOLS}/tools/tableviewer/bin/parse-table |
-    perl \${CIRCOSTOOLS}/tools/tableviewer/bin/make-conf -dir data;
-
-cp -Rv \${CIRCOSTOOLS}/tools/tableviewer/etc .;
-mkdir img;
-circos -conf .;
-
-cp img/tableview.png $output_png;
-cp img/tableview.svg $output_svg;
-]]>
-    </command>
-    <inputs>
-        <param format="tabular" name="input" type="data" label="Data Table" />
-    </inputs>
-    <outputs>
-        <data format="svg" name="output_svg">
-        </data>
-        <data format="png" name="output_png">
-        </data>
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-<![CDATA[
-**What it does**
-
-Very simple table plotter
-
-.. image:: $PATH_TO_IMAGES/tablevie.png
-
-.. class:: warningmark
-
-1. Your tabular data MUST have both a column and row header::
-
-    Data  A  B
-    A     4  2
-    B     0 -2
-
-@REFERENCES@
-]]>
-    </help>
-    <expand macro="citations" />
-</tool>

Binary file static/images/tableview.png has changed

--- a/tool_dependencies.xml	Thu Mar 19 17:58:54 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="circos" version="0.67.5">
-        <repository changeset_revision="cd80b8fe9854" name="package_circos_0_67_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="circostools" version="0.20">
-        <repository changeset_revision="c9392d893389" name="package_circostools_0_20" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>