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planemo upload

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+# Dynamic Galaxy Tool wrappers
+
+Use this repository as a template to develop a dynamic Galaxy tools in one minute!
+
+## Step 1: clone this repository
+
+```bash
+git clone https://github.com/statonlab/dynamic-galaxy-tool-wrappers.git
+``` 
+
+## Step 2: edit tool requirements
+
+Open the `dynamic_tool_wrappers_macros.xml` file and add your tool requirements. **Only tools from the 
+[conda repository](https://anaconda.org/anaconda/repo) can be added as a tool requirement. For example, for a wrapper
+of the **FastQC** tool, go to [https://anaconda.org/anaconda/repo](https://anaconda.org/anaconda/repo) and search for
+`fastqc`. You will get a list of `fastqc` tools. Find the appropriate version and add it as a tool requirement.
+
+Before editing tool requirement:
+
+```xml
+    <xml name="rmarkdown_requirements">
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</requirement>
+    </xml>
+```
+
+After editing tool requirement:
+
+```xml
+    <xml name="rmarkdown_requirements">
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</requirement>
+        <requirement type="package" version="0.11.7">fastqc</requirement>
+    </xml>
+```
+
+
+
+## Step 3: edit template for a specific command line tool
+
+Open the `dynamic_tool_wrappers_macros.xml` file and replace `tool_name` in 
+`<option value="tool_name" selected="false">tool_name</option>` with a valid command line tool name.
+
+```xml
+    <xml name="tool_name">
+        <param type="select" name="tool_name" multiple="false" label="Tool name">
+            <option value="tool_name" selected="false">tool_name</option>
+        </param>
+    </xml>
+```
+
+Use the **FastQC** tool as an example again, the content after replacement would be
+
+```xml
+    <xml name="tool_name">
+        <param type="select" name="tool_name" multiple="false" label="Tool name">
+            <option value="fastqc" selected="false">fastqc</option>
+        </param>
+    </xml>
+```
+
+You can add multiple `tool_name` options if the tool has sub command line tools. For example, 
+for the `samtools` tool, it could be
+
+```xml
+    <xml name="tool_name">
+        <param type="select" name="tool_name" multiple="false" label="Tool name">
+            <option value="samtools view" selected="false">samtols view</option>
+            <option value="samtools sort" selected="false">samtols sort</option>
+            <option value="samtools index" selected="false">samtols index</option>
+        </param>
+    </xml>
+```
+
+## Step 4: edit **tool name** and **tool id** in `dynamic_tool.xml`
+
+Open the `dynamic_tool.xml` file and replace `dynamic_tool` with an appropriate **tool id** and the `dynamic tool` with
+an appropriate **tool name**.
+
+```xml
+<tool id="dynamic_tool" name="dynamic tool" version="1.0.0">
+```
+
+Use the **FastQC** tool as an example, it could be:
+
+```xml
+<tool id="dynamic_fastqc" name="Dynamic FastQC" version="1.0.0">
+```
+
+## Step 5: Publish tool to [ToolShed](https://toolshed.g2.bx.psu.edu/) or [Test ToolShed](https://testtoolshed.g2.bx.psu.edu/)
+
+Please check [planemo's documentation site](http://planemo.readthedocs.io/en/latest/publishing.html) for more details.
+
+* Within the tool directory, `planemo shed_init` command can be used to bootstrap a `.shed.yml` file.
+
+```bash
+planemo shed_init --name=<name>
+                  --owner=<shed_username>
+                  --description=<short description>
+                  [--remote_repository_url=<URL to .shed.yml on github>]
+                  [--homepage_url=<Homepage for tool.>]
+                  [--long_description=<long description>]
+                  [--category=<category name>]*
+```
+
+* **Create tool repository on ToolShed or Test ToolShed**
+
+```bash
+planemo shed_create --shed_target testtoolshed
+```
+
+* **Update a tool repository**
+
+```bash
+planemo shed_diff --shed_target testtoolshed
+```
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