annotate tools/meme/fimo.xml @ 1:cdcb0ce84a1b

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<tool id="meme_fimo" name="FIMO" version="0.0.1">
  <description>- Find Individual Motif Occurrences</description>
  <command interpreter="python">fimo_wrapper.py 'fimo --o "${$html_outfile.files_path}" --verbosity "1"
  
  #if str( $options_type.options_type_selector ) == 'advanced':
  --max-seq-length "${options_type.max_seq_length}" 
  --max-stored-scores "${options_type.max_stored_scores }" 
  --motif-pseudo "${options_type.motif_pseudo}" 
  ${options_type.norc} 
  --output-pthresh "${options_type.output_pthresh}" 

  
  #for $motif in $options_type.motifs:
    --motif "${motif.motif}"
  #end for
  
  #if str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file':
    --bgfile "motif-file"
  #elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file':
    --bgfile "${options_type.bgfile_type.bgfile}"
  #end if
  
  #if str( $options_type.qvalue_type.qvalue_type_selector ) == 'no-qvalue':
    --no-qvalue
  #else:
    --output-qthresh "${options_type.qvalue_type.output_qthresh}"
  #end if
  #end if
  
  "${input_motifs}" 
  
  #if str( $fasta_type.fasta_type_selector ) == 'history':
    "${fasta_type.input_database}"
  #else:
    "${ filter( lambda x: str( x[0] ) == str( $fasta_type.input_database ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][3] }"
  #end if

  '
  
  '${html_outfile.files_path}'
  
  '${html_outfile}'
  
  '${interval_outfile}'
  
  '${txt_outfile}'
  
  '${xml_outfile}'
  
  '${gff_outfile}'
    
  </command>
  <inputs>
    <param format="memexml" name="input_motifs" type="data" label="'MEME output' formatted file"/>
    
    <conditional name="fasta_type">
      <param name="fasta_type_selector" type="select" label="Source for sequence to search">
        <option value="cached">Locally Cached sequences</option>
        <option value="history" selected="true">Sequences from your history</option>
      </param>
      <when value="cached">
        <param name="input_database" type="select" label="Genome to search">
          <options from_data_table="all_fasta">
          </options>
        </param>
      </when>
      <when value="history">
         <param format="fasta" name="input_database" type="data" label="Sequences"/>
      </when>
    </conditional>
    
      <conditional name="options_type">
        <param name="options_type_selector" type="select" label="Options Configuration">
          <option value="basic" selected="true">Basic</option>
          <option value="advanced">Advanced</option>
        </param>
        <when value="basic">
          <!-- do nothing here -->
        </when>
        <when value="advanced">
    
    <conditional name="bgfile_type">
      <param name="bgfile_type_selector" type="select" label="Background file type">
        <option value="motif-file">Use Frequencies from Motif File</option>
        <option value="default" selected="true">Use frequencies from non-redundant database (default)</option>
        <option value="bgfile">Use Frequencies from Background File</option>
      </param>
      <when value="motif-file">
      <!-- do nothing here -->
      </when>
      <when value="default">
      <!-- do nothing here -->
      </when>
      <when value="bgfile">
        <param name="bgfile" type="data" format="txt" optional="True" label="Background Model" />
      </when>
    </conditional>
    
    <repeat name="motifs" title="Limit to specified motif">
      <param name="motif" type="text" value="" label="Specify motif by id" />
    </repeat>
    
    <param name="max_seq_length" type="integer" value="250000000" label="Maximum input sequence length" />
    <param name="max_stored_scores" type="integer" value="100000" label="Maximum score count to store" />
    <param name="motif_pseudo" type="float" value="0.1" label="Pseudocount to add to counts in motif matrix" />
    <param name="norc" label="Do not check reverse complement" type="boolean" truevalue="--norc" falsevalue="" checked="False"/>
    <param name="output_pthresh" type="float" value="1e-4" label="p-value threshold" />
    
    <conditional name="qvalue_type">
      <param name="qvalue_type_selector" type="select" label="q-value options">
        <option value="no-qvalue">Do not compute q-value</option>
        <option value="q-value" selected="true">Compute q-value</option>
      </param>
      <when value="no-qvalue">
      <!-- do nothing here -->
      </when>
      <when value="q-value">
        <param name="output_qthresh" type="float" value="1.0" label="q-value threshold" />
      </when>
    </conditional>
    
      </when>
    </conditional>
    
    <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
      <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
    </param>
  
  </inputs>
  <outputs>
    <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)">
      <actions>
        <conditional name="fasta_type.fasta_type_selector">
          <when value="cached">
            <action type="metadata" name="dbkey">
              <option type="from_data_table" name="all_fasta" column="1" offset="0">
                <filter type="param_value" column="0" value="seq" keep="True"/>
                <filter type="param_value" ref="fasta_type.input_database" column="1"/>
              </option>
            </action>
          </when>
        </conditional>
      </actions>
    </data>
    <data format="tabular" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
      <actions>
        <conditional name="fasta_type.fasta_type_selector">
          <when value="cached">
            <action type="metadata" name="dbkey">
              <option type="from_data_table" name="all_fasta" column="1" offset="0">
                <filter type="param_value" ref="fasta_type.input_database" column="0"/>
              </option>
            </action>
          </when>
        </conditional>
      </actions>
    </data>
    <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
      <actions>
        <conditional name="fasta_type.fasta_type_selector">
          <when value="cached">
            <action type="metadata" name="dbkey">
              <option type="from_data_table" name="all_fasta" column="1" offset="0">
                <filter type="param_value" ref="fasta_type.input_database" column="0"/>
              </option>
            </action>
          </when>
        </conditional>
      </actions>
    </data>
    <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
      <actions>
        <conditional name="fasta_type.fasta_type_selector">
          <when value="cached">
            <action type="metadata" name="dbkey">
              <option type="from_data_table" name="all_fasta" column="1" offset="0">
                <filter type="param_value" ref="fasta_type.input_database" column="0"/>
              </option>
            </action>
          </when>
        </conditional>
      </actions>
    </data>
    <data format="interval" name="interval_outfile" label="${tool.name} on ${on_string} (interval)">
      <actions>
        <conditional name="fasta_type.fasta_type_selector">
          <when value="cached">
            <action type="metadata" name="dbkey">
              <option type="from_data_table" name="all_fasta" column="1" offset="0">
                <filter type="param_value" ref="fasta_type.input_database" column="0"/>
              </option>
            </action>
          </when>
        </conditional>
      </actions>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input_motifs" value="meme/meme/meme_output_xml_1.xml" ftype="memexml"/>
      <param name="fasta_type_selector" value="history"/>
      <param name="input_database" value="phiX.fasta" ftype="fasta"/>
      <param name="options_type_selector" value="basic"/>
      <param name="non_commercial_use" value="True"/>
      <output name="html_outfile" file="meme/fimo/fimo_output_html_1.html" lines_diff="12"/>
      <output name="txt_outfile" file="meme/fimo/fimo_output_txt_1.txt" lines_diff="0"/>
      <output name="gff_outfile" file="meme/fimo/fimo_output_almost-gff_1.txt" lines_diff="0"/>
      <output name="xml_outfile" file="meme/fimo/fimo_output_xml_1.xml" lines_diff="8"/>
      <output name="interval_outfile" file="meme/fimo/fimo_output_interval_1.txt" lines_diff="0"/>
    </test>
  </tests>
  <help>

.. class:: warningmark

**WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. Before using, be sure to review, agree, and comply with the license.**

.. class:: infomark

**To cite FIMO:**
`Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011 Apr 1;27(7):1017-8. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21330290&gt;`_


For detailed information on FIMO, click here_. To view the license_.

.. _here: http://meme.nbcr.net/meme/fimo-intro.html
.. _license: http://meme.nbcr.net/meme/COPYRIGHT.html

  </help>
</tool>