comparison abims_hclustering.xml @ 1:36fc0a87d7fb draft default tip

planemo upload

0:2f7381ee5235

<tool id="abims_hclustering" name="Hierarchical Clustering" version="1.1">

    <description>using ctc R package for java-treeview</description>

    <command interpreter="Rscript">
        abims_hclustering.r file "$input" method $method link $link keep.hclust FALSE normalization $normalization sep "$sep" dec "$dec"
    </command>

    <inputs>
        <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." />
        <param name="method" type="select" label="Distance measure method" help="the distance measure to be used">
            <option value="pearson" selected="true">pearson</option>

        <param name="threshold" type="float" label="threshold" value="0.01" help="max adjusted p.value accepted" />-->
        
    </inputs>

    <outputs>
        <data name="hclust_zip" format="zip" from_work_dir="hclust.zip" label="${input.name[:-4]}.hclust.zip" />
    </outputs>

    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>

    <help>


		
.. class:: infomark

inversions (which are hard to interpret).




-----------
Input files
-----------

+---------------------------+------------+

The complete linkage method finds similar clusters. The single linkage method (which is closely related to the minimal spanning tree) adopts a ‘friends of friends’ clustering strategy.
The other methods can be regarded as aiming for clusters with characteristics somewhere between the single and complete link methods.
Note however, that methods median and centroid are not leading to a monotone distance measure, or equivalently the resulting dendrograms can have so called inversions (which are hard to interpret).


------------
Output files
------------

***.tab.hclust.zip**

**>A part of an example of Data Matrix file input**
	

+--------+------------------+----------------+
| Name   | Bur-eH_FSP_102   | Bur-eH_FSP_22  |	                                       
+========+==================+================+
|M202T601| 91206595.7559783 |106808979.08546 |
+--------+------------------+----------------+
|M234T851| 27249137.275504  |28824971.3177926|  
+--------+------------------+----------------+  

.. image:: hclust.png


    </help>

</tool>

1:36fc0a87d7fb

<tool id="abims_hclustering" name="Hierarchical Clustering" version="1.1.2">

    <description>using ctc R package for java-treeview</description>

    <command interpreter="Rscript"><![CDATA[
        abims_hclustering.r file "$input" method $method link $link keep.hclust FALSE normalization $normalization sep "$sep" dec "$dec" && mv hclust.zip $outputzip
    ]]></command>

    <inputs>
        <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." />
        <param name="method" type="select" label="Distance measure method" help="the distance measure to be used">
            <option value="pearson" selected="true">pearson</option>

        <param name="threshold" type="float" label="threshold" value="0.01" help="max adjusted p.value accepted" />-->
        
    </inputs>

    <outputs>
		<data name="outputzip" format="zip" label="${input.name[:-4]}.heatmap.zip for Java Treeview" />
    </outputs>

    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>

    <help><![CDATA[


		
.. class:: infomark

inversions (which are hard to interpret).




-----------------
Workflow position
-----------------


**Upstream tools**

+---------------------------+----------------------------------------+--------+------------------------+
| Name                      | Output file                            | Format | parameter              |   
+===========================+========================================+========+========================+
|xcms.diffreport            |xset.diffreport.data_matrix.tsv         | Tabular| Data table file        |   
+---------------------------+----------------------------------------+--------+------------------------+
|CAMERA.annotateDiffreport  |xset.annotatediffreport.data_matrix.tsv | Tabular| Data table file        |   
+---------------------------+----------------------------------------+--------+------------------------+
|Anova                      |xset.anova_filtered.tabular             | Tabular| Data table file        |
+---------------------------+----------------------------------------+--------+------------------------+



**Downstream tools**

+---------------------------+-----------------------------------------------+---------------------+
| Name                      | Output file                                   | Format              | 
+===========================+===============================================+=====================+
|Treeview (out of Galaxy)   | cdt,gtr and atr files needed for Java Treeview|Java Treeview formats|
+---------------------------+-----------------------------------------------+---------------------+



-----------
Input files
-----------

+---------------------------+------------+

The complete linkage method finds similar clusters. The single linkage method (which is closely related to the minimal spanning tree) adopts a ‘friends of friends’ clustering strategy.
The other methods can be regarded as aiming for clusters with characteristics somewhere between the single and complete link methods.
Note however, that methods median and centroid are not leading to a monotone distance measure, or equivalently the resulting dendrograms can have so called inversions (which are hard to interpret).



------------
Output files
------------

***.tab.hclust.zip**

**>A part of an example of Data Matrix file input**
	

+--------+------------------+----------------+
| Name   | Bur-eH_FSP_102   | Bur-eH_FSP_22  |
+========+==================+================+
|M202T601| 91206595.7559783 |106808979.08546 |
+--------+------------------+----------------+
|M234T851| 27249137.275504  |28824971.3177926|  
+--------+------------------+----------------+  

.. image:: hclust.png


    </help>

]]></tool>