Revision 0108d6529358e0e3d8a1d6e94c0eb7b5f362db78 authored by John Davis on 22 February 2024, 00:03:00 UTC, committed by John Davis on 22 February 2024, 00:03:00 UTC
1 parent ea9e2fb
fimo.xml
<tool id="meme_fimo" name="FIMO" version="0.0.1">
<requirements><requirement type="package">meme</requirement></requirements>
<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:
"${fasta_type.input_database.fields.path}"
#end if
'
'${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. <http://www.ncbi.nlm.nih.gov/pubmed/21330290>`_
For detailed information on FIMO, click here_. To view the license_.
------
**Citation**
If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
.. _here: http://meme.nbcr.net/meme/fimo-intro.html
.. _license: http://meme.nbcr.net/meme/COPYRIGHT.html
</help>
</tool>
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