comparison sitepro.xml @ 2:45e094f8858f

Add SitePro tool

2:45e094f8858f

<tool id="ceas_sitepro" name="SitePro: Score profile near Intervals" version="0.1.0">
  <description>Draw the score profile near a given interval</description>
  <macros>
    <import>ceas_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>
sitepro 
#if $mode.mode_select == "single"
 -w $mode.wfile -b $mode.bfile 
#elif $mode.mode_select == "multiwig"
 -w $mode.wfile -l $mode.label 
 #for $m in $mode.more
  -w "$m.wig" -l "$m.label"
 #end for
 -b $mode.bfile
#elif $mode.mode_select == "multibed"
 -w $mode.wfile -b $mode.bfile -l $mode.label 
 #for $m in $mode.more
  -b "$m.bfile" -l "$m.label"
 #end for
#end if
--span=$span --pf-res=$pfres --name=$name --dump &amp;> $log  
cat *_dump.txt > $dump
  </command>
  <inputs>
    <param name="name" type="hidden" value="sitepro_out"/>
    <conditional name="mode">
      <param name="mode_select" type="select" label="Sitepro behaviour mode" force_select="true">
	<option value="single"> 1 wiggle vs 1 BED file</option>
	<option value="multiwig"> multiple wiggle vs 1 BED</option>
	<option value="multibed"> multiple BED vs 1 wiggle</option>
      </param>

      <when value="single">
	<param ftype="wig" name="wfile" type="data" label="Wiggle file"/>
	<param ftype="bed" name="bfile" type="data" label="BED file(100,000 lines max)"/>
      </when>

      <when value="multiwig">
	<param format="wig" name="wfile" type="data" label="Wiggle file"/>
	<param name="label" type="text" label="Wiggle label" optional="false" />
	<repeat name="more" title="wiggle file">
	  <param format="wig" name="wig" type="data" label="Select another wiggle file"/>
	  <param name="label" type="text" label="Wiggle label"  optional="false" />
	</repeat>
	<param format="bed" name="bfile" type="data"
	label="BED file"/>
      </when>

      <when value="multibed">
	<param format="bed" name="bfile" type="data" label="BED file(100,000 lines max)"/>
	<param name="label" type="text" label="BED label" optional="false" />
	<repeat name="more" title="BED file">
	  <param format="bed" name="bfile" type="data" label="Select another BED file(100,000 lines max)"/>
	  <param name="label" type="text" label="BED label"  optional="false" />
	</repeat>
	<param format="wig" name="wfile" type="data" label="Wiggle file"/>
      </when>

    </conditional>

    <param name="span" type="integer" label="Span" value="1000">
    	<validator type="in_range" max="1000000" min="100" message="Span is out of range, Span has to be between 100 to 1000000" />
    </param>	
    <param name="pfres" type="integer" label="Profiling Resolution" value="50">
    	<validator type="in_range" max="1000" min="10" message="Profiling Resolution is out of range, Profiling Resolution has to be between 10 to 1000" />
    </param>	
  </inputs>
  <outputs>
    <data name="output" format="pdf" from_work_dir="sitepro_out.pdf"/>
    <data name="log" format="txt" label="sitepro job log" />
    <data name="dump" format="txt" label="txt file with profiles" />
  </outputs>
<tests>
  <test maxseconds="3600" name="Sitepro_1">
    <param name="mode_select" value="single" />
    <param name="wfile" value="treatment.wig" />
    <param name="bfile" value="peaks.bed" />
    <param name="span" value="1000" />
    <param name="pfres" value="50" />
    <output name="output" file="sitepro_1/sitepro_1.pdf" />
    <output name="output" file="sitepro_1/sitepro_1.log" lines_diff = "200" />
    <output name="output" file="sitepro_1/sitepro_1_dump.txt" />
    <output name="log">
        <assert_contents>
          <has_text_matching expression="See sitepro_out.pdf for the graphical result of sitepro" />
        </assert_contents>
    </output>
  </test>
</tests>
  <help>
This tool draws the average score profile around given genomic
sites. It's a module in CEAS package which is written by Hyunjin Gene
Shin, published in Bioinformatics (pubmed id:19689956).

.. class:: infomark

**TIP #1:** If your query does not apper in the pulldown menu for BED Files, please convert your interval files to BED format.

.. class:: infomark

**TIP #2:** You can't use multiple BED files *AND* multiple Wiggle files as input. 

.. class:: infomark

**TIP #3:** The tool can be used to check the signals of your ChIP
sample around certain regions such as Transcription Start Sites, or
Transcription Factor Binding Sites.

.. class:: warningmark

**NEED IMPROVEMENT**

-----

**Parameters**

- **Sitepro behaviour mode** can only be '1 wiggle file against 1 BED
  file', or 'multiple wiggle files against 1 BED file', or '1 wiggle
  file against multiple BED files'.
- **Wiggle label** When 'multi wiggle' mode is selected, you need to assign the labels for every wiggle files which will be shown in the final figure.
- **BED label** When 'multi BED' mode is selected, you need to assign the labels for every BED files which will be shown in the final image.
- **Span** is the distance from the center of each BED region in both directions(+/-) (eg, [c - span, c + span], where c is the center of a region).
- **Profiling resolution** is the resolution to bin the scores in the final image.

-----

**script parameter list of Sitepro**

Options:
  --version             show program's version number and exit
  -h, --help            Show this help message and exit.
  -w WIG, --wig=WIG     input WIG file. WARNING: both fixedStep and
                        variableStep WIG formats are accepted. Multiple WIG
                        files can be given via -w (--wig) individually (eg -w
                        WIG1.wig, -w WIG2.wig). WARNING! multiple wig and bed
                        files are not allowed.
  -b BED, --bed=BED     BED file of regions of interest. (eg, binding sites or
                        motif locations) Multiple BED files can be given via
                        -b (--bed) individually (eg -b BED1.bed -b BED2.bed).
                        WARNING! multiple wig and bed files are not allowed.
  --span=SPAN           Span from the center of each BED region in both
                        directions(+/-) (eg, [c - span, c + span], where c is
                        the center of a region), default:1000 bp
  --pf-res=PF_RES       Profiling resolution, default: 50 bp
  --dir                 If set, the direction (+/-) is considered in
                        profiling. If no strand info given in the BED, this
                        option is ignored.
  --dump                If set, profiles are dumped as a TXT file
  --name=NAME           Name of this run. If not given, the body of the bed
                        file name will be used,
  -l LABEL, --label=LABEL
                        Labels of the wig files. If given, they are used as
                        the legends of the plot and in naming the TXT files of
                        profile dumps; otherwise, the WIG file names will be
                        used as the labels. Multiple labels can be given via
                        -l (--label) individually (eg, -l LABEL1 -l LABEL2).
                        WARNING! The number and order of the labels must be
                        the same as the WIG files.

-----

**Output**

- **PDF** format file.
- Dumped signals within given intervals in **plain text**.

  </help>

</tool>