comparison fimo.xml @ 19:01f5d04846c4 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9

18:c5209f38700d

<tool id="meme_fimo" name="FIMO" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>- Scan a set of sequences for motifs</description>
    <xrefs>
        <xref type="bio.tools">meme_fimo</xref>
    </xrefs>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
@CHECK_NON_COMMERCIAL_USE@
fimo
    -o ./out/
    $scanrc

&& mv ./out/fimo.tsv '${txt_outfile}'
&& mv ./out/fimo.xml '${xml_outfile}'
&& mv ./out/fimo.gff '${gff_outfile}'
    ]]></command>
    <inputs>
        <param name="input_motifs" type="data" format="memexml" label="DREME or MEME output XML file"
               help="DREME or MEME output XML file containing found motifs"/>
        <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>
        <param name="scanrc" label="Check reverse complement strand" type="boolean"
               truevalue="" falsevalue="--norc" checked="False"
               help="Search for motifs also on reverse complement strand"/>
        <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="thresh" type="float" value="1e-4" argument="--thresh"
                label="Output threshold for displaying search results" 
                help="Only output results with a p-value less than the given threshold. To apply set threshold to q-values rather than p-values, set --qv-thresh."/>
                <param name="qv_thresh" label="Apply output threshold to q-values?" argument="--qv-thresh"
                       type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False" 
                       help="Default: apply set threshold on p-values"/>
                <conditional name="bgfile_type">
                    <param name="bgfile_type_selector" type="select" label="Background model selection">
                        <option value="default" selected="true">Use embedded letter frequencies from non-redundant DNA/protein database</option>
                        <option value="motif_file">Use 0-order letter frequencies from motif file</option>
                        <option value="bgfile">Use 0-order letter frequencies from background file</option>
                        <option value="uniform_distr">Use uniform letter frequencies</option>
                    </param>
                    <when value="motif_file" />
                    <when value="default" />
                    <when value="uniform_distr" />
                    <when value="bgfile">
                        <param name="bgfile" type="data" format="txt" optional="True" label="Background model file" help="File must be in Markov background model format (see MEME suite tool fasta-get-markov for details)"/>
                    </when>
                </conditional>
                <param name="max_strand" label="Report best match in case of overlapping matches on both strands?" argument="--max-strand"
                       type="boolean" truevalue="--max-strand" falsevalue="" checked="False" 
                       help="If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score. If the scores are tied, the matching strand is chosen at random (default: report both matches)."/>
                <param name="max_stored_scores" type="integer" value="100000" argument="--max-stored-scores"
                label="Maximum number of scores that will be stored"
                help="Keeping a complete list of scores may exceed available memory. Once the number of stored scores reaches the maximum allowed, the least significant 50% of scores will be dropped. In this case, the list of reported motifs may be incomplete and the q-value calculation will be approximate."/>
                <conditional name="motifs_cond">
                    <param name="motif_selector" type="select" label="Specify single input motifs for scanning?">
                        <option value="no" selected="true">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="no"/>
                    <when value="yes">
                        <repeat name="motifs" title="Supply input motif ID">
                            <param name="motif" type="text" value="" label="Specify motif by id">
                                <validator type="empty_field" />
                                <validator type="regex" message="Value may include alphanumeric characters.">[A-Za-z]+</validator>
                            </param>
                        </repeat>
                    </when>
                </conditional>
                <param name="motif_pseudo" type="float" value="0.1" argument="--motif-pseudo"
                       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="Disable q-value calculation?" 
                       type="boolean" truevalue="--no-qvalue" falsevalue="" checked="False" argument="--no-qvalue"
                       help="The q-value calculation is that of Benjamini and Hochberg (1995) (default: calculate q-value for each p-value)"/>
                <param name="parse_genomic_coords" label="Check each sequence header for UCSC-style genomic coordinates?" 
                       type="boolean" truevalue="--parse-genomic-coord" falsevalue="" checked="False" argument="--parse-genomic-coord"
                       help=" If genomic coordinates are found they will be used as the coordinates in the output."/>
                <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" argument="--psp"
                               label="Select file containing position-specific priors" 
                               help="File should be in MEME PSP format or wiggle format (can be generated by MEME suite tool create-priors)"/>
                        <param name="alpha" type="float" value="1.0" min="0" max="1.0" argument="--alpha"
                               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)"/>
                    </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" argument="--prior-dist"
                               label="Select dataset containing binned distribution of priors"
                               help="This file can be generated using the MEME suite tool create-priors"/>
                    </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>
        <section name="output_options" title="Additional output options">
            <param name="html_outfile" type="boolean" value="False" label="Output HTML file" help="FIMO HTML output file"/>
            <param name="xml_outfile" type="boolean" value="False" label="Output XML file" help="FIMO XML output file"/>

                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
        <data format="txt" name="gff_outfile" label="${tool.name} on ${on_string} (gff)">
            <filter>(output_options['gff_outfile'] is True)</filter>
            <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="html_outfile" value="True"/>
            <param name="xml_outfile" value="True"/>
            <param name="gff_outfile" value="True"/>
            <param name="non_commercial_use" value="True"/>
            <output name="html_outfile" file="fimo_output_test1.html" compare="contains"/>
            <output name="txt_outfile" file="fimo_output_test1.txt" compare="contains"/>
            <output name="xml_outfile" file="fimo_output_test1.xml" compare="contains"/>
            <output name="gff_outfile" file="fimo_output_test1.gff" compare="contains"/>
        </test>
        <test expect_num_outputs="4">
            <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
            <param name="fasta_type_selector" value="history"/>
            <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>

            <param name="bgfile" value="fimo_background_probs_hsa_chrM.txt"/>
            <param name="html_outfile" value="True"/>
            <param name="xml_outfile" value="True"/>
            <param name="gff_outfile" value="True"/>
            <param name="non_commercial_use" value="True"/>
            <output name="html_outfile" file="fimo_output_test2.html" compare="contains"/>
            <output name="txt_outfile" file="fimo_output_test2.txt" compare="contains"/>
            <output name="xml_outfile" file="fimo_output_test2.xml" compare="contains"/>
            <output name="gff_outfile" file="fimo_output_test2.gff" compare="contains"/>
        </test>
        <test expect_num_outputs="3">
            <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
            <param name="fasta_type_selector" value="history"/>
            <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>

            </repeat>
            <param name="html_outfile" value="True"/>
            <param name="xml_outfile" value="True"/>
            <param name="gff_outfile" value="False"/>
            <param name="non_commercial_use" value="True"/>
            <output name="html_outfile" file="fimo_output_test3.html" compare="contains"/>
            <output name="txt_outfile" file="fimo_output_test3.txt" compare="contains"/>
            <output name="xml_outfile" file="fimo_output_test3.xml" compare="contains"/>
        </test>
    </tests>
    <help>

.. class:: warningmark

19:01f5d04846c4

<tool id="meme_fimo" name="FIMO" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>- Scan a set of sequences for motifs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <xrefs>
        <xref type="bio.tools">meme_fimo</xref>
    </xrefs>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
@CHECK_NON_COMMERCIAL_USE@
fimo
    -o ./out/
    $scanrc

&& mv ./out/fimo.tsv '${txt_outfile}'
&& mv ./out/fimo.xml '${xml_outfile}'
&& mv ./out/fimo.gff '${gff_outfile}'
    ]]></command>
    <inputs>
        <param name="input_motifs" type="data" format="memexml" label="DREME or MEME output XML file" help="DREME or MEME output XML file containing found motifs"/>
        <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 name="input_database" type="data" format="fasta" label="Sequences"/>
            </when>
        </conditional>
        <param name="scanrc" type="boolean" truevalue="" falsevalue="--norc" checked="False" label="Check reverse complement strand" help="Search for motifs also on reverse complement strand"/>
        <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 argument="--thresh" type="float" value="1e-4" label="Output threshold for displaying search results" help="Only output results with a p-value less than the given threshold. To apply set threshold to q-values rather than p-values, set --qv-thresh."/>
                <param argument="--qv-thresh" type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False" label="Apply output threshold to q-values?" help="Default: apply set threshold on p-values"/>
                <conditional name="bgfile_type">
                    <param name="bgfile_type_selector" type="select" label="Background model selection">
                        <option value="default" selected="true">Use embedded letter frequencies from non-redundant DNA/protein database</option>
                        <option value="motif_file">Use 0-order letter frequencies from motif file</option>
                        <option value="bgfile">Use 0-order letter frequencies from background file</option>
                        <option value="uniform_distr">Use uniform letter frequencies</option>
                    </param>
                    <when value="motif_file"/>
                    <when value="default"/>
                    <when value="uniform_distr"/>
                    <when value="bgfile">
                        <param name="bgfile" type="data" format="txt" optional="True" label="Background model file" help="File must be in Markov background model format (see MEME suite tool fasta-get-markov for details)"/>
                    </when>
                </conditional>
                <param argument="--max-strand" type="boolean" truevalue="--max-strand" falsevalue="" checked="False" label="Report best match in case of overlapping matches on both strands?" help="If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score. If the scores are tied, the matching strand is chosen at random (default: report both matches)."/>
                <param argument="--max-stored-scores" type="integer" value="100000" label="Maximum number of scores that will be stored" help="Keeping a complete list of scores may exceed available memory. Once the number of stored scores reaches the maximum allowed, the least significant 50% of scores will be dropped. In this case, the list of reported motifs may be incomplete and the q-value calculation will be approximate."/>
                <conditional name="motifs_cond">
                    <param name="motif_selector" type="select" label="Specify single input motifs for scanning?">
                        <option value="no" selected="true">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="no"/>
                    <when value="yes">
                        <repeat name="motifs" title="Supply input motif ID">
                            <param name="motif" type="text" value="" label="Specify motif by id">
                                <validator type="empty_field"/>
                                <validator type="regex" message="Value may include alphanumeric characters.">[A-Za-z]+</validator>
                            </param>
                        </repeat>
                    </when>
                </conditional>
                <param argument="--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 argument="--no-qvalue" type="boolean" truevalue="--no-qvalue" falsevalue="" checked="False" label="Disable q-value calculation?" help="The q-value calculation is that of Benjamini and Hochberg (1995) (default: calculate q-value for each p-value)"/>
                <param name="parse_genomic_coords" argument="--parse-genomic-coord" type="boolean" truevalue="--parse-genomic-coord" falsevalue="" checked="False" label="Check each sequence header for UCSC-style genomic coordinates?" help=" If genomic coordinates are found they will be used as the coordinates in the output."/>
                <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" argument="--psp" type="data" format="txt" label="Select file containing position-specific priors" help="File should be in MEME PSP format or wiggle format (can be generated by MEME suite tool create-priors)"/>
                        <param argument="--alpha" type="float" min="0" max="1.0" value="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)"/>
                    </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" argument="--prior-dist" type="data" format="txt" label="Select dataset containing binned distribution of priors" help="This file can be generated using the MEME suite tool create-priors"/>
                    </when>
                </conditional>
            </when>
        </conditional>
        <param name="non_commercial_use" type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False" label="I certify that I am not using this tool for commercial purposes.">
            <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
        </param>
        <section name="output_options" title="Additional output options">
            <param name="html_outfile" type="boolean" value="False" label="Output HTML file" help="FIMO HTML output file"/>
            <param name="xml_outfile" type="boolean" value="False" label="Output XML file" help="FIMO XML output file"/>

                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
        <data format="gff" name="gff_outfile" label="${tool.name} on ${on_string} (gff)">
            <filter>(output_options['gff_outfile'] is True)</filter>
            <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="html_outfile" value="True"/>
            <param name="xml_outfile" value="True"/>
            <param name="gff_outfile" value="True"/>
            <param name="non_commercial_use" value="True"/>
            <output name="html_outfile" ftype="html">
                <assert_contents>
                    <has_text text="TACTAAYM"/>
                    <has_text text="MEME file name"/>
                </assert_contents>
            </output>
            <output name="txt_outfile">
                <assert_contents>
                    <has_text text="motif_id"/>
                    <has_text text="sequence_name"/>
                    <has_text text="matched_sequence"/>
                    <has_text text="TACTAATA"/>
                </assert_contents>
            </output>
            <output name="xml_outfile" ftype="memexml">
                <assert_contents>
                    <has_text text="sequence-data num-sequences"/>
                    <has_text text="16569"/>
                    <has_text text="Cytosine"/>
                    <has_text text="TACTAACA"/>
                </assert_contents>
            </output>
            <output name="gff_outfile" ftype="gff">
                <assert_contents>
                    <has_text text="gff-version 3"/>
                    <has_text text="TACTAAYM_chrM"/>
                    <has_text text="qvalue"/>
                    <has_text text="nucleotide_motif"/>
                    <has_text text="fimo"/>
                    <has_text text="chrM"/>
                    <has_n_lines n="12"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="4">
            <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
            <param name="fasta_type_selector" value="history"/>
            <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>

            <param name="bgfile" value="fimo_background_probs_hsa_chrM.txt"/>
            <param name="html_outfile" value="True"/>
            <param name="xml_outfile" value="True"/>
            <param name="gff_outfile" value="True"/>
            <param name="non_commercial_use" value="True"/>
            <output name="html_outfile">
                <assert_contents>
                    <has_text text="MOTIF"/>
                    <has_text text="WIDTH"/>
                    <has_text text="TTAACA"/>
                    <has_text text="GAATGT"/>
                </assert_contents>
            </output>
            <output name="txt_outfile">
                <assert_contents>
                    <has_text text="sequence_name"/>
                    <has_text text="motif_id"/>
                    <has_text text="matched_sequence"/>
                    <has_text text="ACTAAYH"/>
                    <has_text text="chrM"/>
                </assert_contents>
            </output>
            <output name="xml_outfile" ftype="memexml">
                <assert_contents>
                    <has_text text="MEME file name"/>
                    <has_text text="pseudocount"/>
                    <has_text text="Not G"/>
                    <has_text text="Keto"/>
                </assert_contents>
            </output>
            <output name="gff_outfile" ftype="gff">
                <assert_contents>
                    <has_text text="gff-version 3"/>
                    <has_text text="ID=ACTAAYH-DREME-1-4-chrM"/>
                    <has_text text="nucleotide_motif"/>
                    <has_text text="fimo"/>
                    <has_text text="chrM"/>
                    <has_n_lines n="12"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
            <param name="fasta_type_selector" value="history"/>
            <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>

            </repeat>
            <param name="html_outfile" value="True"/>
            <param name="xml_outfile" value="True"/>
            <param name="gff_outfile" value="False"/>
            <param name="non_commercial_use" value="True"/>
            <output name="html_outfile">
                <assert_contents>
                    <has_text text="top_buttons"/>
                    <has_text text="database_and_motifs"/>
                    <has_text text="YTAACA"/>
                    <has_text text="ACTAAYH"/>
                    <has_text text="DREME"/>
                </assert_contents>
            </output>
            <output name="txt_outfile">
                <assert_contents>
                    <has_text text="motif_alt_id"/>
                    <has_text text="matched_sequence"/>
                    <has_text text="ACTAAYH"/>
                    <has_text text="ACTAACA"/>
                </assert_contents>
            </output>
            <output name="xml_outfile" ftype="memexml">
                <assert_contents>
                    <has_text text="complement"/>
                    <has_text text="letter"/>
                    <has_text text="16569"/>
                    <has_text text="dna"/>
                    <has_text text="ACTAAYH"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>

.. class:: warningmark