mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
John Chilton
239 lines
9.1 KiB
XML
239 lines
9.1 KiB
XML
<tool id="meme_fimo" name="FIMO" version="0.0.1">
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<requirements><requirement type="package">meme</requirement></requirements>
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<description>- Find Individual Motif Occurrences</description>
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<command interpreter="python">fimo_wrapper.py 'fimo --o "${$html_outfile.files_path}" --verbosity "1"
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#if str( $options_type.options_type_selector ) == 'advanced':
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--max-seq-length "${options_type.max_seq_length}"
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--max-stored-scores "${options_type.max_stored_scores }"
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--motif-pseudo "${options_type.motif_pseudo}"
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${options_type.norc}
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--output-pthresh "${options_type.output_pthresh}"
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#for $motif in $options_type.motifs:
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--motif "${motif.motif}"
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#end for
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#if str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file':
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--bgfile "motif-file"
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#elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file':
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--bgfile "${options_type.bgfile_type.bgfile}"
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#end if
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#if str( $options_type.qvalue_type.qvalue_type_selector ) == 'no-qvalue':
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--no-qvalue
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#else:
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--output-qthresh "${options_type.qvalue_type.output_qthresh}"
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#end if
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#end if
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"${input_motifs}"
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#if str( $fasta_type.fasta_type_selector ) == 'history':
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"${fasta_type.input_database}"
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#else:
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"${fasta_type.input_database.fields.path}"
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#end if
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'
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'${html_outfile.files_path}'
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'${html_outfile}'
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'${interval_outfile}'
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'${txt_outfile}'
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'${xml_outfile}'
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'${gff_outfile}'
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</command>
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<inputs>
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<param format="memexml" name="input_motifs" type="data" label="'MEME output' formatted file"/>
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<conditional name="fasta_type">
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<param name="fasta_type_selector" type="select" label="Source for sequence to search">
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<option value="cached">Locally Cached sequences</option>
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<option value="history" selected="true">Sequences from your history</option>
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</param>
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<when value="cached">
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<param name="input_database" type="select" label="Genome to search">
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<options from_data_table="all_fasta">
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</options>
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</param>
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</when>
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<when value="history">
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<param format="fasta" name="input_database" type="data" label="Sequences"/>
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</when>
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</conditional>
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<conditional name="options_type">
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<param name="options_type_selector" type="select" label="Options Configuration">
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<option value="basic" selected="true">Basic</option>
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<option value="advanced">Advanced</option>
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</param>
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<when value="basic">
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<!-- do nothing here -->
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</when>
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<when value="advanced">
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<conditional name="bgfile_type">
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<param name="bgfile_type_selector" type="select" label="Background file type">
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<option value="motif-file">Use Frequencies from Motif File</option>
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<option value="default" selected="true">Use frequencies from non-redundant database (default)</option>
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<option value="bgfile">Use Frequencies from Background File</option>
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</param>
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<when value="motif-file">
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<!-- do nothing here -->
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</when>
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<when value="default">
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<!-- do nothing here -->
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</when>
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<when value="bgfile">
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<param name="bgfile" type="data" format="txt" optional="True" label="Background Model" />
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</when>
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</conditional>
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<repeat name="motifs" title="Limit to specified motif">
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<param name="motif" type="text" value="" label="Specify motif by id" />
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</repeat>
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<param name="max_seq_length" type="integer" value="250000000" label="Maximum input sequence length" />
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<param name="max_stored_scores" type="integer" value="100000" label="Maximum score count to store" />
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<param name="motif_pseudo" type="float" value="0.1" label="Pseudocount to add to counts in motif matrix" />
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<param name="norc" label="Do not check reverse complement" type="boolean" truevalue="--norc" falsevalue="" checked="False"/>
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<param name="output_pthresh" type="float" value="1e-4" label="p-value threshold" />
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<conditional name="qvalue_type">
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<param name="qvalue_type_selector" type="select" label="q-value options">
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<option value="no-qvalue">Do not compute q-value</option>
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<option value="q-value" selected="true">Compute q-value</option>
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</param>
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<when value="no-qvalue">
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<!-- do nothing here -->
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</when>
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<when value="q-value">
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<param name="output_qthresh" type="float" value="1.0" label="q-value threshold" />
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</when>
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</conditional>
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</when>
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</conditional>
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<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">
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<validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
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</param>
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</inputs>
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<outputs>
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<data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)">
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<actions>
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<conditional name="fasta_type.fasta_type_selector">
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<when value="cached">
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<action type="metadata" name="dbkey">
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<option type="from_data_table" name="all_fasta" column="1" offset="0">
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<filter type="param_value" column="0" value="seq" keep="True"/>
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<filter type="param_value" ref="fasta_type.input_database" column="1"/>
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</option>
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</action>
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</when>
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</conditional>
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</actions>
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</data>
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<data format="tabular" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
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<actions>
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<conditional name="fasta_type.fasta_type_selector">
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<when value="cached">
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<action type="metadata" name="dbkey">
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<option type="from_data_table" name="all_fasta" column="1" offset="0">
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<filter type="param_value" ref="fasta_type.input_database" column="0"/>
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</option>
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</action>
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</when>
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</conditional>
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</actions>
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</data>
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<data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
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<actions>
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<conditional name="fasta_type.fasta_type_selector">
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<when value="cached">
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<action type="metadata" name="dbkey">
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<option type="from_data_table" name="all_fasta" column="1" offset="0">
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<filter type="param_value" ref="fasta_type.input_database" column="0"/>
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</option>
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</action>
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</when>
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</conditional>
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</actions>
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</data>
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<data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
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<actions>
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<conditional name="fasta_type.fasta_type_selector">
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<when value="cached">
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<action type="metadata" name="dbkey">
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<option type="from_data_table" name="all_fasta" column="1" offset="0">
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<filter type="param_value" ref="fasta_type.input_database" column="0"/>
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</option>
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</action>
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</when>
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</conditional>
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</actions>
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</data>
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<data format="interval" name="interval_outfile" label="${tool.name} on ${on_string} (interval)">
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<actions>
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<conditional name="fasta_type.fasta_type_selector">
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<when value="cached">
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<action type="metadata" name="dbkey">
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<option type="from_data_table" name="all_fasta" column="1" offset="0">
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<filter type="param_value" ref="fasta_type.input_database" column="0"/>
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</option>
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</action>
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</when>
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</conditional>
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</actions>
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</data>
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</outputs>
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<tests>
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<test>
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<param name="input_motifs" value="meme/meme/meme_output_xml_1.xml" ftype="memexml"/>
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<param name="fasta_type_selector" value="history"/>
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<param name="input_database" value="phiX.fasta" ftype="fasta"/>
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<param name="options_type_selector" value="basic"/>
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<param name="non_commercial_use" value="True"/>
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<output name="html_outfile" file="meme/fimo/fimo_output_html_1.html" lines_diff="12"/>
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<output name="txt_outfile" file="meme/fimo/fimo_output_txt_1.txt" lines_diff="0"/>
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<output name="gff_outfile" file="meme/fimo/fimo_output_almost-gff_1.txt" lines_diff="0"/>
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<output name="xml_outfile" file="meme/fimo/fimo_output_xml_1.xml" lines_diff="8"/>
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<output name="interval_outfile" file="meme/fimo/fimo_output_interval_1.txt" lines_diff="0"/>
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</test>
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</tests>
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<help>
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.. class:: warningmark
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**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.**
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.. class:: infomark
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**To cite FIMO:**
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`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>`_
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For detailed information on FIMO, click here_. To view the license_.
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------
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**Citation**
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If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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.. _here: http://meme.nbcr.net/meme/fimo-intro.html
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.. _license: http://meme.nbcr.net/meme/COPYRIGHT.html
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</help>
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</tool>
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