--- a/fimo.xml	Sat Apr 09 08:32:23 2022 +0000
+++ b/fimo.xml	Thu Aug 29 10:19:40 2024 +0000
@@ -1,12 +1,12 @@
-<tool id="meme_fimo" name="FIMO" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<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>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 @CHECK_NON_COMMERCIAL_USE@
 fimo
@@ -56,8 +56,7 @@
 && 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"/>
+        <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>
@@ -65,16 +64,14 @@
             </param>
             <when value="cached">
                 <param name="input_database" type="select" label="Genome to search">
-                    <options from_data_table="all_fasta" />
+                    <options from_data_table="all_fasta"/>
                 </param>
             </when>
             <when value="history">
-                <param format="fasta" name="input_database" type="data" label="Sequences"/>
+                <param name="input_database" type="data" format="fasta" 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"/>
+        <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>
@@ -82,12 +79,8 @@
             </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"/>
+                <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>
@@ -95,19 +88,15 @@
                         <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="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."/>
+                <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>
@@ -117,21 +106,15 @@
                     <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="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."/>
+                <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>
@@ -139,12 +122,8 @@
                     </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)"/>
+                        <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">
@@ -154,14 +133,12 @@
                     </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"/>
+                        <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" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
+        <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">
@@ -199,7 +176,7 @@
                 </conditional>
             </actions>
         </data>
-        <data format="txt" name="gff_outfile" label="${tool.name} on ${on_string} (gff)">
+        <data format="gff" name="gff_outfile" label="${tool.name} on ${on_string} (gff)">
             <filter>(output_options['gff_outfile'] is True)</filter>
             <actions>
                 <conditional name="fasta_type.fasta_type_selector">
@@ -239,10 +216,39 @@
             <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"/>
+            <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"/>
@@ -256,10 +262,41 @@
             <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"/>
+            <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"/>
@@ -277,9 +314,32 @@
             <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"/>
+            <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>