view conservation.xml @ 4:e426a7a39562 default tip

Set version on Conservation Plot tool

<tool name="Conservation Plot" id="ceas_conservation" version="0.1.0">
  <description>Calculates the PhastCons scores in several intervals sets</description>
  <version_command>conservation_plot.py --version</version_command>
  <macros>
    <import>ceas_macros.xml</import>
  </macros>
  <expand macro="requirements_bx" />
  <stdio>
    <exit_code range="1:"  level="fatal"   description="Failed" />
  </stdio>
  <command>
conservation_plot.py 
#if $phastcons.phastcons_src == 'cached':
 -d "${phastcons.gv.fields.path}"
#else:
 -d "$phastcons.phasdb.extra_files_path"
#end if
-w $size 
#if $inputs.labeling == 'auto':
  #echo str($inputs.bfiles).replace(',',' ')
#else
 #for $m in $inputs.more
   $m.bfile  -l "$m.blabel"
 #end for
#end if
&amp;&gt;  $log
  </command>
  <inputs>
    <conditional name="inputs">
      <param name="labeling" type="select" label="input bed files">
        <option value="auto">automatically labeled inputs</option>
        <option value="manual">user labeled inputs</option>
      </param>
      <when value="auto">
        <param name="bfiles" type="data" format="interval" label="bed files" multiple="true"/>
      </when>
      <when value="auto">
        <repeat name="more" title="interval file" min="1">
          <param name="bfile" type="data" format="interval" label="Select another interval file(100,000 lines max)"/>
          <param name="blabel" type="text" label="BED file label" help="label on the figure" optional="false"/>
        </repeat>
      </when>
    </conditional>
    <param name="size" type="integer" label="window size around the center" value="3000">
    	<validator type="in_range" max="10000" min="100" message="window size is out of range, window size has to be between 100 to 10000" />
    </param>
    <conditional name="phastcons">
      <param name="phastcons_src" type="select" label="Source for phasdb phastcons scores">
        <option value="cached" selected="true">A builtin phasdb</option>
        <option value="history">A phasdb from your history</option>
      </param>
      <when value="cached">
        <param name="gv" type="select" label="PHASDB - UCSC genome/assembly version">
          <options from_data_table="cistrome_conservation">
            <filter type="unique_value" column="0" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="phasdb" type="data" format="cistrome_phasdb" label="PHASDB phastcons scores"/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data name="output" format="pdf" from_work_dir="tmp.pdf" />
    <data name="log" format="txt" label="conservation job log"/>
  </outputs>
<tests>
  <test>
    <param name="labeling" value="auto"/>
    <param name="bfile" value="peaks.bed" />
    <param name="blabel" value="conservation_1" />
    <param name="size" value="1000" />
    <param name="phastcons_src" value="history"/>
    <param name="phasdb" value="hg19_phasdb.zip" ftype="cistrome_phasdb" />
    <output name="log">
        <assert_contents>
          <has_text_matching expression="extract phastcons scores" />
        </assert_contents>
    </output>
  </test>
</tests>
  <help>
This tool plots the PhastCons scores prfiles in several BED
files. It's based on conservation_plot.py script in Tao Liu's
library. Original code is written by Ying Lei, then modified by
Jaqueline Wentz.

.. class:: infomark

**Tip:** If you see red Xs, check the BED input file first. Perhaps, the BED file contains some abnormal chromosome names.  

.. class:: infomark

**Tip:** For best performance, please make sure the regions in the BED file are centered at peak summits.

-----

**Parameters**

- **Title** Conservation Plot Tool
- **Interval file** is a BED file normally centered at peak summit. 
- **BED file label** is the label marked in the legend of the final figure.
- **more** You can add more BED files and labels.
- **Window size** is the regions around peak centers to extract PhastCons scores.
- **UCSC genome version** must be selected according to your BED files.

-----

**script parameter list for conservation_plot.py**

conservation_plot.py

Draw conservation plot for many bed files.

Options:
  --version             show program's version number and exit
  -H HEIGHT, --height=HEIGHT
                        height of plot
  -W WIDTH, --width=WIDTH
                        width of plot
  -w W                  window width centered at middle of bed
                        regions,default: 1000
  -t TITLE, --title=TITLE
                        title of the figure. Default: 'Average Phastcons
                        around the Center of Sites'
  -d PHASDB, --phasdb=PHASDB
                        The directory to store phastcons scores in the server
  -l BEDLABEL, --bed-label=BEDLABEL
                        the BED file labels in the figure. No space is
                        allowed. This option should be used same times as -w
                        option, and please input them in the same order as BED
                        files. default: will use the BED file filename as
                        labels.
  -h, --help            Show this help message and exit.


  </help>

</tool>