Mercurial > repos > jbrayet > maketssdist

changeset 66:6c05e086f736 draft

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Deleted selected files
author jbrayet
date Thu, 13 Aug 2015 05:38:55 -0400
parents 526de88709a8
children b48276da909c
files makeTSSdist_wrapper.xml tool_dependencies.xml
diffstat 2 files changed, 0 insertions(+), 123 deletions(-) [+]
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--- a/makeTSSdist_wrapper.xml	Thu Aug 13 05:22:28 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,117 +0,0 @@
-<tool id="makeTSSdist" name="MakeTSSdist" version="1.0">
-  <description>Get peak distribution around TSS</description>
-  <requirements>
-    <requirement type="package" version="3.16.0">hmisc</requirement>
-  </requirements>
-  <command interpreter="bash">
-
-#if str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #makeTSSdist_wrapper.sh -f $inputfile -l $left -o $outputPNG -r $right -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #makeTSSdist_wrapper.sh -f $inputfile -l $left -o $outputPDF -r $right -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # makeTSSdist_wrapper.sh -f $inputfile -c $controlfile -o $outputPNG -l $left -r $right -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # makeTSSdist_wrapper.sh -f $inputfile -c $controlfile -o $outputPDF -l $left -r $right -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # makeTSSdist_wrapper.sh -f $inputfile -e $regfile -l $left -o $outputPNG -r $right -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # makeTSSdist_wrapper.sh -f $inputfile -e $regfile -l $left -o $outputPDF -r $right -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "yes" #makeTSSdist_wrapper.sh -f $inputfile -c $controlfile -l $left -o $outputPNG -r $right -u $stats -v $input_organism.version -e $regfile -p 0 #else # makeTSSdist_wrapper.sh -f $inputfile -c $controlfile -l $left -o $outputPDF -r $right -u $stats -v $input_organism.version -e $regfile -p 1 #end if
-  </command>
-  <inputs>
-     <param name="inputfile" type="data" label="ChIP peaks" value="ChIP peaks File" format="bed"/>
-     <conditional name="use_control">
-       <param name="use_control_selector" type="select" label="Use control data">
-         <option value="no" selected="true">No</option>
-         <option value="yes">Yes</option>
-       </param>
-       <when value="yes">
-         <param name="controlfile" type="data" label="Control peaks" value="Control peaks File" format="bed"/>
-       </when>
-     </conditional>
-     <param name="left" type="integer" label="Step (bp)" value="1000"/>
-     <param name="right" type="integer" label="length of the region +-TSS to consider (bp)" value="50000"/>
-     <conditional name="input_organism">
-       <param name="input_organism_selector" type="select" label="Select organism">
-         <option value="Human" selected="true">Homo sapiens</option>
-         <option value="Mouse">Mus musculus</option>
-         <option value="Zebrafish">Zebrafish (Danio rerio)</option>
-         <option value="XTropicalis">X.Tropicalis</option>
-         <option value="Bacteria/MycoTube">M. tuberculosis</option>
-       </param>
-       <when value="Human">
-         <param name="version" type="select" label="Select genome vesion">
-           <option value="hg19" selected="true">hg19</option>
-           <option value="hg18">hg18</option>
-         </param>
-       </when>
-       <when value="Mouse">
-         <param name="version" type="select" label="Select genome vesion">
-           <option value="mm8" >mm8</option>
-           <option value="mm9" selected="true">mm9</option>
-           <option value="mm10" >mm10</option>
-         </param>
-       </when>
-       <when value="Zebrafish">
-         <param name="version" type="select" label="Select genome vesion">
-           <option value="zv9" selected="true">zv9</option>
-         </param>
-       </when>
-       <when value="XTropicalis">
-         <param name="version" type="select" label="Select genome vesion">
-           <option value="xenTro2" >xenTro2</option>
-           <option value="xenTro3" selected="true">xenTro3</option>
-         </param>
-       </when>
-       <when value="Bacteria/MycoTube">
-         <param name="version" type="select" label="Select genome vesion">
-           <option value="H37Rv" selected="true">H37Rv</option>
-         </param>
-       </when>
-     </conditional>
-     <conditional name="use_reg">
-       <param name="use_reg_selector" type="select" label="Use transcriptomic data (up- and down- regulated genes)">
-         <option value="no" selected="true">No</option>
-         <option value="yes">Yes</option>
-       </param>
-       <when value="yes">
-         <param name="regfile" type="data" label="File with information about gene regulation" value="Regulation data" format="txt"/>
-       </when>
-     </conditional>
-     <param name="if_PDF" type="boolean" label="Do you want to have a PDF image (default PNG)?" truevalue="1" falsevalue="0" checked="False"/>
-   </inputs>
-   <outputs>
-     <data name="outputPNG" format="png" label="Peak location distribution (png)">
-       <filter>(if_PDF == 0)</filter>
-     </data>
-     <data name="outputPDF" format="pdf" label="Peak location distribution (pdf)">
-       <filter>(if_PDF == True)</filter>
-     </data>
-     <data name="stats" format="tabular" label="Peak location distribution (stats)"/>
-   </outputs>
-   <tests>
-     <test>
-       <param name="inputfile" value="peaks_test.bed"/>
-       <param name="use_control_selector" value="yes"/>
-       <param name="controlfile" value="peaks_control.bed"/>
-       <param name="left" value="1000"/>
-       <param name="right" value="50000"/>
-       <param name="input_organism_selector" value="Mouse"/>
-       <param name="version" value="mm9"/>
-       <param name="use_reg_selector" value="yes"/>
-       <param name="regfile" value="Probesets_FC1.5_10022011.txt"/>
-       <param name="if_PDF" value="1"/>
-       <output name="outputPDF" file="test_makeTSSdist_1.dat" ftype="pdf"/>
-       <output name="stats" file="test_makeTSSdist_2.dat" ftype="tabular"/>
-     </test>
-   </tests>
-   <help>
-**What it does**
-
-This tool creates a .png file with distribution of peaks around gene TSS
-
-  </help>
-  <citations>
-    <citation type="bibtex">@article{Boeva01102012,
-      author = {Boeva, Valentina and Lermine, Alban and Barette, Camille and Guillouf, Christel and Barillot, Emmanuel},
-      title = {Nebula—a web-server for advanced ChIP-seq data analysis},
-      volume = {28},
-      number = {19},
-      pages = {2517-2519},
-      year = {2012},
-      doi = {10.1093/bioinformatics/bts463},
-      URL = {http://bioinformatics.oxfordjournals.org/content/28/19/2517.abstract},
-      eprint = {http://bioinformatics.oxfordjournals.org/content/28/19/2517.full.pdf+html},
-      journal = {Bioinformatics}
-      }</citation>
-    </citations>
-</tool>
--- a/tool_dependencies.xml	Thu Aug 13 05:22:28 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="hmisc" version="3.16.0">
-        <repository changeset_revision="aeacbc355d4c" name="hmisc_3_16_0" owner="jbrayet" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>