comparison fimo.xml @ 5:eca84de658b0 draft

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4:cd54079f0f72

<tool id="meme_fimo" name="FIMO" version="4.11.0.2">
    <description>- Scan a set of sequences for motifs.</description>
    <requirements>
        <requirement type="package" version="6.9.3">imagemagick</requirement>
        <requirement type="package" version="4.11.0">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:

                #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}"

                        <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>
                </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">

            <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="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>

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_.

5:eca84de658b0

<tool id="meme_fimo" name="FIMO" version="4.11.0.3">
    <description>- Scan a set of sequences for motifs.</description>
    <requirements>
        <requirement type="package" version="6.9.3">imagemagick</requirement>
        <requirement type="package" version="4.11.0">meme</requirement>
    </requirements>
    <command>
        <![CDATA[
            mkdir -p output &&
            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:

                #if str($options_type.motifs_cond.motifs_selector) == 'no':
                    #for $motif in $options_type.motifs:
                        --motif "${motif.motif}"
                    #end for
                #end if
                --output_separate_motifs ${options_type.output_separate_motifs}
                --motif_pseudo "${options_type.motif_pseudo}"
                ${options_type.no_qvalue}
                ${options_type.norc}
                #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == 'yes':
                    --parse_genomic_coord 'yes'
                    --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords}
                #end if
                #if str($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}"

                        <repeat name="motifs" title="Limit to specified motif">
                            <param name="motif" type="text" value="" label="Specify motif by id" />
                        </repeat>
                    </when>
                </conditional>
                <param name="output_separate_motifs" type="select" label="Output a dataset per motif?" help="Output a collection consisting of a separate dataset for each motif in the input">
                    <option value="no" selected="true">No</option>
                    <option value="yes">Yes</option>
                </param>
                <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" />
                <conditional name="parse_genomic_coord_cond">
                    <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="select">
                        <option value="no" selected="true">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="yes">
                        <param name="remove_duplicate_coords" type="boolean" truevalue="yes" falsevalue="no" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates" />
                    </when>
                    <when value="no"/>
                </conditional>
                <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>
                </conditional>
            </actions>
        </data>
        <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
            <filter>options_type['output_separate_motifs'] == 'no'</filter>
            <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>
        <collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
            <filter>options_type['output_separate_motifs'] == 'yes'</filter>
        </collection>
        <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
            <actions>
                <conditional name="fasta_type.fasta_type_selector">
                    <when value="cached">
                        <action type="metadata" name="dbkey">

            <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" compare="contains"/>
            <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="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" compare="contains"/>
            <output name="interval_outfile" file="fimo_output_interval_2.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="parse_genomic_coord" value="--parse_genomic_coord"/>
            <param name="remove_duplicate_coords" value="yes"/>
            <param name="output_separate_motifs" value="yes"/>
            <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_collection name="motifs" type="list">
                <element name="MOTIF1.gff" file="motif1.gff" ftype="gff" compare="contains"/>
            </output_collection>
            <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/>
            <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
        </test>
    </tests>
    <help>

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).

.. class:: infomark

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