--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fimo.xml	Tue Dec 22 17:01:51 2015 -0500
@@ -0,0 +1,250 @@
+<tool id="meme_fimo" name="FIMO" version="4.11.0.0">
+    <description>- Scan a set of sequences for motifs.</description>
+    <requirements>
+        <requirement type="package" version="4.11.0.0">meme</requirement>
+    </requirements>
+    <command>
+        <![CDATA[
+            python $__tool_directory__/fimo_wrapper.py
+            --input_motifs "${input_motifs}"
+            #if str($fasta_type.fasta_type_selector) == 'history':
+                --input_fasta "${fasta_type.input_database}"
+            #else:
+                --input_fasta "${fasta_type.input_database.fields.path}"
+            #end if
+            --options_type $options_type.options_type_selector
+            #if str($options_type.options_type_selector) == 'advanced':
+                --alpha "${options_type.alpha}"
+                #if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file':
+                    --bgfile "motif-file"
+                #elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile':
+                    --bgfile "${options_type.bgfile_type.bgfile}"
+                #end if
+                ${options_type.max_strand}
+                --max_stored_scores "${options_type.max_stored_scores}"
+                #if str($options_type.motifs_cond.motifs_selector) == 'no':
+                    #for $motif in $options_type.motifs:
+                        --motif "${motif.motif}"
+                    #end for
+                #end if
+                --motif_pseudo "${options_type.motif_pseudo}"
+                ${options_type.no_qvalue}
+                ${options_type.norc}
+                ${options_type.parse_genomic_coord}
+                #if str($options_type.psp_cond.psp_selector) == 'yes':
+                    --input_psp "${input_psp}"
+                #end if
+                #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes':
+                    --input_prior_dist "${input_prior_dist}"
+                #end if
+                ${options_type.qv_thresh}
+                --thresh ${options_type.thresh}
+            #end if
+            --output_path '${html_outfile.files_path}'
+            --html_output "${html_outfile}"
+            --interval_output '${interval_outfile}'
+            --txt_output "${txt_outfile}"
+            --xml_output "${xml_outfile}"
+            --gff_output "${gff_outfile}"
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_motifs" type="data" format="memexml" 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" />
+                </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" />
+            <when value="advanced">
+                <param name="alpha" type="float" value="1.0" min="0" max="1.0" label="Alpha parameter for calculating position specific priors" help="Represents the fraction of all transcription factor binding sites that are binding sites for the TF of interest (must be between 0 and 1)."/>
+                <conditional name="bgfile_type">
+                    <param name="bgfile_type_selector" type="select" label="Background file type">
+                        <option value="default" selected="true">Use frequencies embedded in the application from the non-redundant database</option>
+                        <option value="motif_file">Use frequencies from motif file</option>
+                        <option value="bgfile">Use frequencies from background file</option>
+                    </param>
+                    <when value="motif_file" />
+                    <when value="default" />
+                    <when value="bgfile">
+                        <param name="bgfile" type="data" format="txt" optional="True" label="Background Model" help="File must be in MEME background file format."/>
+                    </when>
+                </conditional>
+                <param name="max_strand" label="If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score" type="boolean" truevalue="--max_strand" falsevalue="" checked="False" help="If the scores are tied, the matching strand is chosen at random.  Leave unchecked to report both matches."/>
+                <param name="max_stored_scores" type="integer" value="100000" label="Maximum number of scores that will be stored" />
+                <conditional name="motifs_cond">
+                    <param name="motifs_selector" type="select" label="Use all motifs in input?">
+                        <option value="yes" selected="true">Yes</option>
+                        <option value="no">No</option>
+                    </param>
+                    <when value="yes"/>
+                    <when value="no">
+                        <repeat name="motifs" title="Limit to specified motif">
+                            <param name="motif" type="text" value="" label="Specify motif by id" />
+                        </repeat>
+                    </when>
+                </conditional>
+                <param name="motif_pseudo" type="float" value="0.1" label="Pseudocount to add to counts in motif matrix" help="A pseudocount to be added to each count in the motif matrix, after first multiplying by the corresponding background frequency"/>
+                <param name="no_qvalue" label="Do not compute a q-value for each p-value" type="boolean" truevalue="--no_qvalue" falsevalue="" checked="True" help="The q-value calculation is that of Benjamini and Hochberg (1995)."/>
+                <param name="norc" label="Do not score the reverse complement DNA strand" type="boolean" truevalue="--norc" falsevalue="" checked="False" />
+                <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="boolean" truevalue="--parse_genomic_coord" falsevalue="" checked="False" />
+                <conditional name="psp_cond">
+                    <param name="psp_selector" type="select" label="Use position-specific priors?">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no"/>
+                    <when value="yes">
+                        <param name="input_psp" type="data" format="txt" label="Select dataset containing position specific priors" help="Format must be meme psp or wiggle."/>
+                    </when>
+                </conditional>
+                <conditional name="prior_dist_cond">
+                    <param name="prior_dist_selector" type="select" label="Use binned distribution of priors?">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no"/>
+                    <when value="yes">
+                        <param name="input_prior_dist" type="data" format="txt" label="Select dataset containing binned distribution of priors"/>
+                    </when>
+                </conditional>
+                <param name="qv_thresh" label="Use q-values for the output threshold" type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False" help="Leave unchecked to use p-values for the output threshold."/>
+                <param name="thresh" type="float" value="1e-4" label="Output threshold for displaying search results" help="Only search results with a p-value less than the threshold will be output. The threshold can be set to use q-values rather than p-values via the option above."/>
+            </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_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="fimo_output_html_1.html" compare="contains"/>
+            <output name="txt_outfile" file="fimo_output_txt_1.txt" compare="contains"/>
+            <output name="gff_outfile" file="fimo_output_almost-gff_1.txt" compare="contains"/>
+            <output name="xml_outfile" file="fimo_output_xml_1.xml" lines_diff="8"/>
+            <output name="interval_outfile" file="fimo_output_interval_1.txt" compare="contains"/>
+        </test>
+        <test>
+            <param name="input_motifs" value="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="advanced"/>
+            <param name="non_commercial_use" value="True"/>
+            <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/>
+            <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
+            <output name="gff_outfile" file="fimo_output_almost-gff_2.txt" compare="contains"/>
+            <output name="xml_outfile" file="fimo_output_xml_2.xml" lines_diff="8"/>
+            <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
+        </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.**
+
+FIMO scans a sequence database for individual matches to each of the motifs you provide (sample output for motifs and sequences).
+The name FIMO stands for 'Find Individual Motif Occurrences'.  The program searches a database of sequences for occurrences of
+known motifs, treating each motif independently.  Motifs must be in MEME Motif Format.  You can define the statistical threshold
+(p-value) for motifs and whether FIMO scans just the given sequences or their reverse complements (where applicable), too.
+
+.. class:: infomark
+
+For detailed information on FIMO, click here_, or view the license_.
+
+.. _here: http://meme-suite.org/doc/fimo.html?man_type=web
+.. _license: http://meme-suite.org/doc/copyright.html?man_type=web
+
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btr064</citation>
+    </citations>
+</tool>