meme_fimo: fimo.xml comparison

comparison fimo.xml @ 13:4eb02864e5df draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b

author	iuc
date	Thu, 17 May 2018 14:11:00 -0400
parents	c470b36b592d
children	c1a9a297ba8b

comparison

equal deleted inserted replaced

-:02f6ad791bbf
+:4eb02864e5df
 <tool id="meme_fimo" name="FIMO" version="@WRAPPER_VERSION@.0">
-<description>- Scan a set of sequences for motifs.</description>
+<description>- Scan a set of sequences for motifs</description>
 <macros>
 <import>macros.xml</import>
 </macros>
 <expand macro="requirements" />
 <command detect_errors="exit_code"><![CDATA[
-mkdir -p output &&
+fimo
-python '$__tool_directory__/fimo_wrapper.py'
+-o ./out/
---input_motifs '${input_motifs}'
+$scanrc
-#if str($fasta_type.fasta_type_selector) == 'history':
+#if str( $options_type.options_type_selector ) == 'advanced':
---input_fasta '${fasta_type.input_database}'
+--thresh $options_type.thresh
-#else:
+$options_type.qv_thresh
---input_fasta '${fasta_type.input_database.fields.path}'
+#if str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif_file':
-#end if
+--bgfile --motif--
---options_type $options_type.options_type_selector
+#elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'bgfile':
-#if str($options_type.options_type_selector) == 'advanced':
+--bgfile $options_type.bgfile_type.bgfile
---alpha '${options_type.alpha}'
+#elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'uniform_distr':
-#if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file':
+--bgfile --uniform--
---bgfile 'motif-file'
+#end if
-#elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile':
+$options_type.max_strand
---bgfile '${options_type.bgfile_type.bgfile}'
+--max-stored-scores $options_type.max_stored_scores
+#if str( $options_type.motifs_cond.motif_selector) == 'yes':
+#for $motif in $options_type.motifs_cond.motifs:
+--motif $motif.motif
+#end for
+#end if
+--motif-pseudo $options_type.motif_pseudo
+$options_type.no_qvalue
+$options_type.parse_genomic_coords
+#if str( $options_type.psp_cond.psp_selector ) == 'yes':
+--psp $options_type.psp_cond.input_psp
+--alpha $options_type.psp_cond.alpha
+#end if
+#if str( $options_type.prior_dist_cond.prior_dist_selector ) == 'yes':
+--prior-dist $options_type.prior_dist_cond.input_prior_dist
+#end if
 #end if
-${options_type.max_strand}
+'$input_motifs'
---max_stored_scores '${options_type.max_stored_scores}'
+#if str($fasta_type.fasta_type_selector) == 'history':
-#if str($options_type.motifs_cond.motifs_selector) == 'no':
+'${fasta_type.input_database}'
-#for $motif in $options_type.motifs:
+#else:
---motif '${motif.motif}'
+'${fasta_type.input_database.fields.path}'
-#end for
 #end if
---output_separate_motifs ${options_type.output_separate_motifs}
+&& mv ./out/fimo.html '${html_outfile}'
---motif_pseudo '${options_type.motif_pseudo}'
+&& mv ./out/fimo.txt '${txt_outfile}'
-${options_type.no_qvalue}
+&& mv ./out/fimo.xml '${xml_outfile}'
-${options_type.norc}
+&& mv ./out/fimo.gff '${gff_outfile}'
-#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 '${input_prior_dist}'
-#end if
-${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"/>
+<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>
 <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="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)."/>
+<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 file type">
+<param name="bgfile_type_selector" type="select" label="Background model selection">
-<option value="default" selected="true">Use frequencies embedded in the application from the non-redundant database</option>
+<option value="default" selected="true">Use embedded letter frequencies from non-redundant DNA/protein database</option>
-<option value="motif_file">Use frequencies from motif file</option>
+<option value="motif_file">Use 0-order letter frequencies from motif file</option>
-<option value="bgfile">Use frequencies from background 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" help="File must be in MEME background file format."/>
+<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="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_strand" label="Report best match in case of overlapping matches on both strands?" argument="--max-strand"
-<param name="max_stored_scores" type="integer" value="100000" label="Maximum number of scores that will be stored" />
+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="motifs_selector" type="select" label="Use all motifs in input?">
+<param name="motif_selector" type="select" label="Specify single input motifs for scanning?">
-<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="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="no"/>
 <when value="yes">
-<param name="remove_duplicate_coords" type="select" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates">
+<repeat name="motifs" title="Supply input motif ID">
-<option value="no" selected="true">No</option>
+<param name="motif" type="text" value="" label="Motif ID" />
-<option value="yes">Yes</option>
+</repeat>
-</param>
+</when>
-</when>
+</conditional>
-<when value="no"/>
+<param name="motif_pseudo" type="float" value="0.1" argument="--motif-pseudo"
-</conditional>
+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" label="Select dataset containing position specific priors" help="Format must be meme psp or wiggle."/>
+<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" label="Select dataset containing binned distribution of priors"/>
+<param name="input_prior_dist" type="data" format="txt" argument="--prior-dist"
-</when>
+label="Select dataset containing binned distribution of priors"
-</conditional>
+help="This file can be generated using the MEME suite tool create-priors"/>
-<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."/>
+</when>
-<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."/>
+</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"/>
+<param name="gff_outfile" type="boolean" value="False" label="Output GFF file" help="FIMO GFF output file"/>
+</section>
 </inputs>
 <outputs>
+<data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
+<actions>
+<conditional name="fasta_type.fasta_type_selector">
+<when value="cached">
+<action type="metadata" name="dbkey">
+<option type="from_data_table" name="all_fasta" column="1" offset="0">
+<filter type="param_value" ref="fasta_type.input_database" column="0"/>
+</option>
+</action>
+</when>
+</conditional>
+</actions>
+</data>
 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)">
+<filter>(output_options['html_outfile'] is True)</filter>
 <actions>
 <conditional name="fasta_type.fasta_type_selector">
 <when value="cached">
 <action type="metadata" name="dbkey">
 <option type="from_data_table" name="all_fasta" column="1" offset="0">
 </action>
 </when>
 </conditional>
 </actions>
 </data>
-<data format="tabular" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
+<data format="txt" name="gff_outfile" label="${tool.name} on ${on_string} (gff)">
+<filter>(output_options['gff_outfile'] is True)</filter>
 <actions>
 <conditional name="fasta_type.fasta_type_selector">
 <when value="cached">
 <action type="metadata" name="dbkey">
 <option type="from_data_table" name="all_fasta" column="1" offset="0">
 </action>
 </when>
 </conditional>
 </actions>
 </data>
-<data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
+<data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
-<filter>options_type['options_type_selector'] == 'basic' or (options_type['options_type_selector'] == 'advanced' and options_type['output_separate_motifs'] == 'no')</filter>
+<filter>(output_options['xml_outfile'] is True)</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">
 </action>
 </when>
 </conditional>
 </actions>
 </data>
-<collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}">
-<discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
-<filter>options_type['options_type_selector'] == 'advanced' and options_type['output_separate_motifs'] == 'yes'</filter>
-</collection>
-<data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
-<actions>
-<conditional name="fasta_type.fasta_type_selector">
-<when value="cached">
-<action type="metadata" name="dbkey">
-<option type="from_data_table" name="all_fasta" column="1" offset="0">
-<filter type="param_value" ref="fasta_type.input_database" column="0"/>
-</option>
-</action>
-</when>
-</conditional>
-</actions>
-</data>
-<data format="interval" name="interval_outfile" label="${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>
+<test expect_num_outputs="4">
-<param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
+<param name="input_motifs" value="meme_fimo_input_1.xml" ftype="memexml"/>
 <param name="fasta_type_selector" value="history"/>
-<param name="input_database" value="phiX.fasta" ftype="fasta"/>
+<param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
+<param name="scanrc" value="true"/>
 <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_html_1.html" compare="contains"/>
+<output name="html_outfile" file="fimo_output_test1.html" lines_diff="20"/>
-<output name="txt_outfile" file="fimo_output_txt_1.txt" compare="contains"/>
+<output name="txt_outfile" file="fimo_output_test1.txt"/>
-<output name="gff_outfile" file="fimo_output_almost-gff_1.txt" compare="contains"/>
+<output name="xml_outfile" file="fimo_output_test1.xml" lines_diff="20"/>
-<output name="xml_outfile" file="fimo_output_xml_1.xml" compare="contains"/>
+<output name="gff_outfile" file="fimo_output_test1.gff"/>
-<output name="interval_outfile" file="fimo_output_interval_1.txt" compare="contains"/>
 </test>
-<test>
+<test expect_num_outputs="4">
-<param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
+<param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
 <param name="fasta_type_selector" value="history"/>
-<param name="input_database" value="phiX.fasta" ftype="fasta"/>
+<param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
+<param name="scanrc" value="true"/>
 <param name="options_type_selector" value="advanced"/>
+<param name="bgfile_type_selector" value="bgfile"/>
+<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_html_2.html" compare="contains"/>
+<output name="html_outfile" file="fimo_output_test2.html" lines_diff="20"/>
-<output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
+<output name="txt_outfile" file="fimo_output_test2.txt"/>
-<output name="gff_outfile" file="fimo_output_almost-gff_2.txt" compare="contains"/>
+<output name="xml_outfile" file="fimo_output_test2.xml" lines_diff="20"/>
-<output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/>
+<output name="gff_outfile" file="fimo_output_test2.gff"/>
-<output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
 </test>
-<test>
+<test expect_num_outputs="3">
-<param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
+<param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
 <param name="fasta_type_selector" value="history"/>
-<param name="input_database" value="phiX.fasta" ftype="fasta"/>
+<param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
+<param name="scanrc" value="true"/>
 <param name="options_type_selector" value="advanced"/>
-<param name="parse_genomic_coord" value="yes"/>
+<param name="thresh" value="0.01"/>
-<param name="remove_duplicate_coords" value="yes"/>
+<param name="bgfile_type_selector" value="uniform_distr"/>
-<param name="output_separate_motifs" value="yes"/>
+<param name="motif_selector" value="yes"/>
+<repeat name="motifs">
+<param name="motif" value="ACTAAYH"/>
+</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_html_2.html" compare="contains"/>
+<output name="html_outfile" file="fimo_output_test3.html" lines_diff="20"/>
-<output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
+<output name="txt_outfile" file="fimo_output_test3.txt"/>
-<output_collection name="motifs" type="list">
+<output name="xml_outfile" file="fimo_output_test3.xml" lines_diff="20"/>
-<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>
 .. class:: warningmark

Mercurial > repos > iuc > meme_fimo

comparison fimo.xml @ 13:4eb02864e5df draft