comparison tools/plotting/venn_list.xml @ 3:6aae6bc0802d draft

Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub

2:c96bef0643dc

<tool id="venn_list" name="Venn Diagram" version="0.0.3">
  <description>from lists</description>
  <command interpreter="python">
venn_list.py
#if $universe.type_select=="implicit":
  - -
#else:

"$main_lab"
#for $s in $sets:
  $s.set $s.set.ext "$s.lab"
#end for
$PDF</command>
  <inputs>
    <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/>
    <conditional name="universe">
       <param name="type_select" type="select" label="Implicit or explicit full ID list?">
         <option value="explicit">Explicit</option>

    </repeat>
  </inputs>
  <outputs>
    <data format="pdf" name="PDF" />
  </outputs>
  <requirements>
    <requirement type="python-module">rpy</requirement>
    <requirement type="python-module">Bio</requirement>
  </requirements>
  <tests>
    <!-- Doesn't seem to work properly, manages to get two sets, both
         with same FASTA file, but second with default "Group" label.
    <test>
      <param name="type_select" value="explicit"/>
      <param name="main" value="venn_list.tabular" ftype="tabular"/>
      <param name="main_lab" value="Some Proteins"/>
      <param name="set" value="rhodopsin_proteins.fasta"/>
      <param name="lab" value="Rhodopsins"/>
      <output name="PDF" file="venn_list1.pdf" ftype="pdf"/>
    </test>
    -->
    <!-- Can't use more than one repeat value in tests (yet)
    <test>
      <param name="type_select" value="explicit"/>
      <param name="main" value="venn_list.tabular" ftype="tabular"/>
      <param name="main_lab" value="Some Proteins"/>

The Venn Diagrams are drawn using Gordon Smyth's limma package from
R/Bioconductor, http://www.bioconductor.org/

The R library is called from Python via rpy, http://rpy.sourceforge.net/

This tool uses Biopython to read SFF files. If you use this tool with
SFF files in scientific work leading to a publication, please cite the
Biopython application note:

Cock et al 2009. Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

3:6aae6bc0802d

<tool id="venn_list" name="Venn Diagram" version="0.0.6">
  <description>from lists</description>
  <requirements>
    <requirement type="python-module">rpy</requirement>
    <requirement type="python-module">Bio</requirement>
  </requirements>
  <command interpreter="python">
venn_list.py
#if $universe.type_select=="implicit":
  - -
#else:

"$main_lab"
#for $s in $sets:
  $s.set $s.set.ext "$s.lab"
#end for
$PDF</command>
  <stdio>
    <!-- Anything other than zero is an error -->
    <exit_code range="1:" />
    <exit_code range=":-1" />
  </stdio>
  <inputs>
    <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/>
    <conditional name="universe">
       <param name="type_select" type="select" label="Implicit or explicit full ID list?">
         <option value="explicit">Explicit</option>

    </repeat>
  </inputs>
  <outputs>
    <data format="pdf" name="PDF" />
  </outputs>
  <tests>
    <!-- Doesn't seem to work properly, manages to get two sets, both
         with same FASTA file, but second with default "Group" label. -->
    <test>
      <param name="type_select" value="explicit"/>
      <param name="main" value="venn_list.tabular" ftype="tabular"/>
      <param name="main_lab" value="Some Proteins"/>
      <param name="set" value="rhodopsin_proteins.fasta"/>
      <param name="lab" value="Rhodopsins"/>
      <output name="PDF" file="venn_list1.pdf" ftype="pdf"/>
    </test>
    <!-- Can't use more than one repeat value in tests (yet)
    <test>
      <param name="type_select" value="explicit"/>
      <param name="main" value="venn_list.tabular" ftype="tabular"/>
      <param name="main_lab" value="Some Proteins"/>

The Venn Diagrams are drawn using Gordon Smyth's limma package from
R/Bioconductor, http://www.bioconductor.org/

The R library is called from Python via rpy, http://rpy.sourceforge.net/

If you use this Galaxy tool in work leading to a scientific publication please
cite:

Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
Galaxy tools and workflows for sequence analysis with applications
in molecular plant pathology. PeerJ 1:e167
http://dx.doi.org/10.7717/peerj.167

This tool uses Biopython to read and write SFF files, so you may also wish to
cite the Biopython application note (and Galaxy too of course):

Cock et al 2009. Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.