comparison rnachipintegrator_wrapper.xml @ 1:5f69a2c1b9c9 draft

Uploaded version 1.0.0.0.

0:d9c1f2133124

<?xml version="1.0" encoding="utf-8"?>
<tool id="rnachipintegrator_wrapper" name="RnaChipIntegrator" version="@VERSION@-0">
  <description>Integrated analysis of gene expression data and ChIP data</description>
  <macros>
    <import>rnachipintegrator_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="version_command" />
  <command interpreter="bash">rnachipintegrator_wrapper.sh
  #if str( $analysis_options.peak_type ) == "summits"
    #if str( $analysis_options.window ) != ""
    --window=$analysis_options.window
    #end if
    #if str( $analysis_options.cutoff ) != ""
    --cutoff=$analysis_options.cutoff
    #end if
  #end if
  #if str( $analysis_options.peak_type ) == "regions"
    #if str( $analysis_options.edge_cutoff ) != ""
    --edge-cutoff=$analysis_options.edge_cutoff
    #end if
    #if str( $analysis_options.number ) != ""
    --number=$analysis_options.number
    #end if
    #if (str( $analysis_options.promoter_start ) != "" and str( $analysis_options.promoter_end ))
    --promoter_region=$analysis_options.promoter_start,$analysis_options.promoter_end
    #end if
    #if $analysis_options.pad_output
    --pad
    #end if
  #end if
  $rnaseq $chipseq
  --output_xls $xls_output
  #if $results_as_zip
  --zip_file $zip_file
  #else
    #if str( $analysis_options.peak_type ) == "summits"
    --summit_outputs $peaks_to_transcripts_out $tss_to_summits_out
    #end if
    #if str( $analysis_options.peak_type ) == "regions"
    --peak_outputs $transcripts_to_edges_out
                   $transcripts_to_edges_summary
                   $tss_to_edges_out
                   $tss_to_edges_summary
    #end if
  #end if
  </command>
  <inputs>
    <param format="tabular" name="rnaseq" type="data" label="Gene expression data file" />
    <param format="tabular" name="chipseq" type="data" label="ChIP peaks data file" />
  <conditional name="analysis_options">
    <!-- user must specify if ChIP peaks are summits or regions -->
    <param name="peak_type" type="select" label="ChIP peaks are"
	   help="Options and outputs depend on whether ChIP data are summits or regions">
      <option value="summits">summits</option>
      <option value="regions">regions</option>
    </param>
    <when value="summits">
      <param name="window" type="integer" value="20000" optional="true"
	     label="Maximum distance a peak can be from each transcript
		    TSS before being omitted from analysis" />
      <param name="cutoff" type="integer" value="130000" optional="true"
	     label="Maximum distance a transcript TSS can be from each
		    peak before being omitted from the analysis" />
    </when>
    <when value="regions">
      <param name="edge_cutoff" type="integer" value="10000" optional="true"
	     label="Maximum distance a transcript edge can be from the
		    peak edge before being omitted from the analysis"
	     help="Set to zero to indicate that no cut off should be applied" />
      <param name="number" type="integer" value="4" optional="true"
	     label="Maximum number of transcripts per peak to report from
		    from the analysis" />
      <param name="promoter_start" type="integer" value="-10000" optional="true"
	     label="Start of promoter region with respect to gene TSS" />
      <param name="promoter_end" type="integer" value="2500" optional="true"
	     label="End of promoter region with respect to gene TSS" />
      <param name="pad_output" type="boolean" checked="false" truevalue="yes"
	     label="Output same number of lines for each peak"
	     help="Add blank lines in output for peaks with fewer than maximum number
		   of hits (--pad)" />
    </when>
  </conditional>
    <param name="results_as_zip" type="boolean" checked="false" truevalue="yes"
           label="Put output tab-delimited files into a single zip archive" />
  </inputs>
  <outputs>
    <!-- Always produce XLS output -->
    <data format="xls" name="xls_output"
	  label="All RnaChipIntegrator analyses for ${rnaseq.name} vs ${chipseq.name} (Excel spreadsheet)" />
    <!-- Outputs only produced for summit data -->
    <data format="tabular" name="peaks_to_transcripts_out"
	  label="Nearest summits to transcripts for ${rnaseq.name} vs ${chipseq.name}" >
      <filter>analysis_options['peak_type'] == "summits"</filter>
      <filter>results_as_zip is False</filter>
    </data>
    <data format="tabular" name="tss_to_summits_out"
	  label="Nearest TSS to summits for ${rnaseq.name} vs ${chipseq.name}" >
      <filter>analysis_options['peak_type'] == "summits"</filter>
      <filter>results_as_zip is False</filter>
    </data>
    <!-- Outputs only produced for peak data -->
    <data format="tabular" name="transcripts_to_edges_out"
	  label="Nearest transcripts to peak edges for ${rnaseq.name} vs ${chipseq.name}" >
      <filter>analysis_options['peak_type'] == "regions"</filter>
      <filter>results_as_zip is False</filter>
    </data>
    <data format="tabular" name="transcripts_to_edges_summary"
	  label="Nearest transcripts to peak edges (summary) for ${rnaseq.name} vs ${chipseq.name}" >
      <filter>analysis_options['peak_type'] == "regions"</filter>
      <filter>results_as_zip is False</filter>
    </data>
    <data format="tabular" name="tss_to_edges_out"
	  label="Nearest TSS to peak edges for ${rnaseq.name} vs ${chipseq.name}" >
      <filter>analysis_options['peak_type'] == "regions"</filter>
      <filter>results_as_zip is False</filter>
    </data>
    <data format="tabular" name="tss_to_edges_summary"
	  label="Nearest TSS to peak edges (summary) for ${rnaseq.name} vs ${chipseq.name}" >
      <filter>analysis_options['peak_type'] == "regions"</filter>
      <filter>results_as_zip is False</filter>
    </data>
    <data format="zip" name="zip_file"
	  label="All tab-delimited files for ${rnaseq.name} vs ${chipseq.name} (zip file)" >
      <filter>results_as_zip is True</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="rnaseq" value="ExpressionData.txt" ftype="tabular" />
      <param name="chipseq" value="ChIP_summits.txt" ftype="tabular" />
      <param name="peak_type" value="summits" />
      <param name="window" value="20000" />
      <param name="cutoff" value="130000" />
      <!-- 
      **NB** outputs have to be specified in order that they appear in the
      tool (which is the order they will be written to the history) - the
      test framework seems to use the order and ignores the "name" attribute
      -->
      <output name="xls_output" file="summits.xls" compare="sim_size" />
      <output name="peaks_to_transcripts_out" file="peaks_to_transcripts.out" ftype="tabular" />
      <output name="tss_to_summits_out" file="tss_to_summits.out" ftype="tabular" />
    </test>
    <test>
      <param name="rnaseq" value="ExpressionData.txt" ftype="tabular" />
      <param name="chipseq" value="ChIP_peaks.txt" ftype="tabular" />
      <param name="peak_type" value="regions" />
      <param name="edge_cutoff" value="130000" />
      <!-- 
      **NB** outputs have to be specified in order that they appear in the
      tool (which is the order they will be written to the history) - the
      test framework seems to use the order and ignores the "name" attribute
      -->
      <output name="xls_output" file="peaks.xls" compare="sim_size" />
      <output name="transcripts_to_edges_out" file="transcripts_to_edges.out" ftype="tabular" />
      <output name="transcripts_to_edges_summary" file="transcripts_to_edges.summary" ftype="tabular" />
      <output name="tss_to_edges_out" file="tss_to_edges.out" ftype="tabular" />
      <output name="tss_to_edges_summary" file="tss_to_edges.summary" ftype="tabular" />
    </test>
  </tests>
  <help>

.. class:: infomark

**What it does**

Run RnaChipIntegrator to perform integrated analyses of gene expression
and ChIP data, identifying the nearest ChIP peaks to each transcript
and vice versa.

For ChIP peaks defined as regions the following analyses are performed:

 * **TranscriptsToPeakEdges**: reports the nearest transcripts with the smallest
   distance from either their TSS or TES to the nearest peak edge.

 * **TSSToPeakEdges**: reports the nearest transcripts with the smallest distance
   from their TSS to the nearest peak edge.

For ChIP peaks defined as summits:

 * **TSSToSummits**: reports the nearest transcripts with the smallest distance
   from the TSS to the nearest peak summit.

 * **PeaksToTranscripts**: reports the nearest peak summits with the smallest
   distance to either the TSS or TES of each transcript.

The program was originally written specifically for ChIP-Seq and RNA-Seq data
but works equally well for ChIP-chip and microarray expression data, and can
also be used to integrate any set of genomic features (e.g. canonical genes,
CpG islands) with expression data.

RnaChipIntgerator can be obtained from
http://fls-bioinformatics-core.github.com/RnaChipIntegrator/

-------------

.. class:: infomark

**Input**

The expression data must be in a tab-delimited file with the following columns
of data for each genomic feature (one feature per line):

====== ========== ======================================================================
Column Name       Description
====== ========== ======================================================================
     1 ID         Name used to identify the feature in the output
     2 chr        Chromosome name
     3 start      Start position of the feature
     4 end        End position of the feature
     5 strand     Must be either '+' or '-'
     6 diff_expr  Optional: indicates feature is differentially expressed (1) or not (0)
====== ========== ======================================================================

The ChIP-seq data must be in a tab-delimited file with 3 columns of data for each
ChIP peak (one per line):

====== ========== ======================================================================
Column Name       Description
====== ========== ======================================================================
     1 chr        Chromosome name (must match one of those in expression data file)
     2 start      Start position of the peak 
     3 end        End position of the peak (start + 1 for summit data)
====== ========== ======================================================================

The ChIP peak data can be either the summit (in which case 'end' - 'start' = 1) or the
entire extent of the binding region (with 'start' and 'end' indicating the limits).

-------------

.. class:: infomark

**Output**

The outputs from this tool vary depending on the type of data that is input, however
generally there is one tab-delimited results file for each analysis described above
in the **What it does** section (some analyses output a second file with just the
"best" hits).

A history item will be generated for each output file, unless the option to put them
into a single zip archive is selected; this archive file will have to be downloaded
and unzipped on your local machine. It is recommended that you refer to the
RnaChipIntegrator documentation for information on the contents of each output file:
https://github.com/fls-bioinformatics-core/RnaChipIntegrator/blob/master/doc/MANUAL.markdown

In addition an Excel spreadsheet (with one page for each analysis performed) is always
produced.

-------------

.. class:: infomark

developed by this group, and is documented at
http://fls-bioinformatics-core.github.com/RnaChipIntegrator/

Please kindly acknowledge the Bioinformatics Core Facility if you use this tool.
  </help>
</tool>

1:5f69a2c1b9c9

<?xml version="1.0" encoding="utf-8"?>
<tool id="rnachipintegrator_wrapper" name="RnaChipIntegrator" version="@VERSION@.0">
  <description>Integrated analysis of 'gene' and 'peak' data</description>
  <macros>
    <import>rnachipintegrator_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="version_command" />
  <command interpreter="bash"><![CDATA[
  rnachipintegrator_wrapper.sh
  #if $peaks_in.metadata.chromCol
    --peak_cols=${peaks_in.metadata.chromCol},${peaks_in.metadata.startCol},${peaks_in.metadata.endCol}
  #end if
  #if str( $cutoff ) != ""
    --cutoff=$cutoff
  #else
    --cutoff=0
  #end if
  #if str( $number ) != ""
    --number=$number
  #end if
  --promoter_region=$promoter_start,$promoter_end
  --edge=$edge
  $diff_expressed_only
  --xlsx_file "$xlsx_out"
  --output_files "$peaks_per_feature_out" "$features_per_peak_out"
  #if $output.compact_format
    --compact
  #else
    #if $output.summary
      --summary_files "$peaks_per_feature_summary" "$features_per_peak_summary"
    #end if
    ${output.pad_output}
  #end if
  "$features_in" "$peaks_in"
  ]]></command>
  <inputs>
    <param format="tabular" name="features_in" type="data"
	   label="Genes/genomic features" />
    <param format="tabular" name="peaks_in" type="data"
	   label="Peaks/regions" />
    <expand macro="analysis_options" />
    <param name="diff_expressed_only" type="boolean"
	   truevalue="--only-DE" falsevalue="" checked="false"
	   label="Only consider genes which are flagged as differentially
		  expressed"
           help="NB input feature data must include differential expression
		 flags (--only-DE)" />
    <expand macro="output_options" />
  </inputs>
  <outputs>
    <!-- Always produce XLSX output -->
    <data format="xlsx" name="xlsx_out"
	  label="All RnaChipIntegrator analyses: ${features_in.name} vs ${peaks_in.name} (Excel spreadsheet)" />
    <data format="tabular" name="peaks_per_feature_out"
	  label="Nearest peaks to each gene: ${features_in.name} vs ${peaks_in.name}" />
    <data format="tabular" name="features_per_peak_out"
	  label="Nearest genes to each peak: ${features_in.name} vs ${peaks_in.name}" />
    <data format="tabular" name="peaks_per_feature_summary"
	  label="Nearest peaks to each gene (summary): ${features_in.name} vs ${peaks_in.name}" >
      <filter>output['compact_format'] is False</filter>
      <filter>output['summary'] is True</filter>
    </data>
    <data format="tabular" name="features_per_peak_summary"
	  label="Nearest gene to each peak (summary): ${features_in.name} vs ${peaks_in.name}" >
      <filter>output['compact_format'] is False</filter>
      <filter>output['summary'] is True</filter>
    </data>
  </outputs>
  <tests>
    <!--
	RnaChipIntegrator +name=test +cutoff=130000 +promoter_region=-10000,2500 +xlsx +compact features.txt summits.txt
    -->
    <test>
      <param name="features_in" value="features.txt" ftype="tabular" />
      <param name="peaks_in" value="summits.txt" ftype="tabular" />
      <param name="cutoff" value="130000" />
      <param name="promoter_start" value="-10000" />
      <param name="promoter_end" value="2500" />
      <output name="xlsx_out" file="summits.xlsx" compare="sim_size" />
      <output name="peaks_per_feature_out" ftype="tabular"
	      file="summits_per_feature.out" />
      <output name="features_per_peak_out" ftype="tabular"
	      file="features_per_summit.out" />
    </test>
    <!--
	RnaChipIntegrator +name=test +cutoff=130000 +promoter_region=-10000,2500 +xlsx +compact features.txt peaks.txt
    -->
    <test>
      <param name="features_in" value="features.txt" ftype="tabular" />
      <param name="peaks_in" value="peaks.txt" ftype="tabular" />
      <param name="cutoff" value="130000" />
      <param name="promoter_start" value="-10000" />
      <param name="promoter_end" value="2500" />
      <output name="xlsx_out" file="peaks1.xlsx" compare="sim_size" />
      <output name="peaks_per_feature_out" ftype="tabular"
	      file="peaks_per_feature1.out" />
      <output name="features_per_peak_out" ftype="tabular"
	      file="features_per_peak1.out" />
    </test>
    <!--
	RnaChipIntegrator +name=test +cutoff=130000 +xlsx features.txt peaks.txt
    -->
    <test>
      <param name="features_in" value="features.txt" ftype="tabular" />
      <param name="peaks_in" value="peaks.txt" ftype="tabular" />
      <param name="cutoff" value="130000" />
      <param name="compact_format" value="false" />
      <output name="xlsx_out" file="peaks2.xlsx" compare="sim_size" />
      <output name="peaks_per_feature_out" ftype="tabular"
	      file="peaks_per_feature2.out" />
      <output name="features_per_peak_out" ftype="tabular"
	      file="features_per_peak2.out" />
    </test>
    <!--
	RnaChipIntegrator +name=test +cutoff=130000 +only-DE +xlsx +compact features.txt peaks.txt
    -->
    <test>
      <param name="features_in" value="features.txt" ftype="tabular" />
      <param name="peaks_in" value="peaks.txt" ftype="tabular" />
      <param name="cutoff" value="130000" />
      <param name="diff_expressed_only" value="true" />
      <output name="xlsx_out" file="peaks3.xlsx" compare="sim_size" />
      <output name="peaks_per_feature_out" ftype="tabular"
	      file="peaks_per_feature3.out" />
      <output name="features_per_peak_out" ftype="tabular"
	      file="features_per_peak3.out" />
    </test>
    <!--
	RnaChipIntegrator +name=test +cutoff=130000 +promoter_region=-10000,2500 +xlsx +summary features.txt peaks.txt
    -->
    <test>
      <param name="features_in" value="features.txt" ftype="tabular" />
      <param name="peaks_in" value="peaks.txt" ftype="tabular" />
      <param name="cutoff" value="130000" />
      <param name="compact_format" value="false" />
      <param name="summary" value="true" />
      <param name="pad_output" value="true" />
      <output name="xlsx_out" file="peaks4.xlsx" compare="sim_size" />
      <output name="peaks_per_feature_out" ftype="tabular"
	      file="peaks_per_feature4.out" />
      <output name="features_per_peak_out" ftype="tabular"
	      file="features_per_peak4.out" />
      <output name="peaks_per_feature_summary" ftype="tabular"
	      file="peaks_per_feature4.summary" />
      <output name="features_per_peak_summary" ftype="tabular"
	      file="features_per_peak4.summary" />
    </test>
  </tests>
  <help>

.. class:: infomark

**What it does**

Performs integrated analyses of genes (or other genomic feature data)
gainst a set of peaks (e.g. ChIP data), identifying the nearest peaks to
each feature and vice versa.

The program was originally written specifically for ChIP-Seq and RNA-Seq
data but works equally well for ChIP-chip and microarray expression data,
and can also be used to integrate any set of genomic features (e.g.
canonical genes, CpG islands) with expression data.

RnaChipIntegrator can be obtained from
https://pypi.python.org/pypi/RnaChipIntegrator/

-------------

.. class:: infomark

**Input**

The gene data must be in a tabular file with the following columns
of data for each gene or genomic feature (one gene per line):

====== ========== ======================================================================
Column Name       Description
====== ========== ======================================================================
     1 ID         Name used to identify the gene in the output
     2 chr        Chromosome name
     3 start      Start position of the gene
     4 end        End position of the gene
     5 strand     Must be either '+' or '-'
     6 diff_expr  Optional: indicates gene is differentially expressed (1) or not (0)
====== ========== ======================================================================

The peak data must be in a tabular file with at least 3 columns of data
for each peak (one peak per line):

====== ========== =================================
Column Name       Description
====== ========== =================================
     1 chr        Chromosome name
     2 start      Start position of the peak 
     3 end        End position of the peak
====== ========== =================================

If peak data is in ``bed`` format then the tool will automatically
assign the correct columns, otherwise the first three columns of data
will be used.

-------------

.. class:: infomark

**Outputs**

The key outputs from the tool are two lists compromising the nearest
peaks for each gene, and the nearest gene for each peak (one dataset
for each list).

There are two formats for reporting: "compact" and "full":

 * **Compact output** reports all the hits for each peak or gene on
   a single line of output;
 * **Full output** reports each peak/gene pair on a separate line
   (i.e. a multi-line output format).

In "full" output mode, additional options are available:

 * The output files can be "padded" with extra (empty) lines to ensure
   that there are always the same number of lines for each peak or
   gene, if fewer than the requested number of hits are found.
 * "Summary" datasets can also be requested, which include just the
   nearest peak reported for each gene (and vice versa).

In either mode these data will also be output in a single MS Excel file,
which contains one sheet per result set.

.. class:: warning

Using "compact" output with the number of hits limited to more than 4
peak/gene pairs (or with no limit at all) can result in a large number
of columns in the output files, which in some versions of Galaxy will
not be properly displayed. However the data files themselves should be
okay.

-------------

.. class:: informark

**More information**

It is recommended that you refer to the ``RnaChipIntegrator``
documentation for information on the contents of each output file:

* http://rnachipintegrator.readthedocs.org/en/latest/

-------------

.. class:: infomark

developed by this group, and is documented at
http://fls-bioinformatics-core.github.com/RnaChipIntegrator/

Please kindly acknowledge the Bioinformatics Core Facility if you use this tool.
  </help>
  <expand macro="citations" />
</tool>