/tools/meme/fimo.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 238 lines · 198 code · 36 blank · 4 comment · 0 complexity · f6615e228480ced549e7a90313c6475f MD5 · raw file
- <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>