Mercurial > repos > iuc > meme_dreme

changeset 6:fd05b142b3a3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
author iuc
date Thu, 29 Aug 2024 10:19:55 +0000
parents f33d77dcacce
children
files dreme.xml macros.xml test-data/dreme_output_test1.html test-data/dreme_output_test1.txt test-data/dreme_output_test1.xml test-data/dreme_output_test2.html test-data/dreme_output_test2.txt test-data/dreme_output_test2.xml test-data/fimo_output_test1.gff test-data/fimo_output_test1.html test-data/fimo_output_test1.txt test-data/fimo_output_test1.xml test-data/fimo_output_test2.gff test-data/fimo_output_test2.html test-data/fimo_output_test2.txt test-data/fimo_output_test2.xml test-data/fimo_output_test3.html test-data/fimo_output_test3.txt test-data/fimo_output_test3.xml
diffstat 19 files changed, 74 insertions(+), 662 deletions(-) [+]
line wrap: on
line diff
--- a/dreme.xml	Sat Apr 09 08:32:58 2022 +0000
+++ b/dreme.xml	Thu Aug 29 10:19:55 2024 +0000
@@ -1,11 +1,9 @@
-<tool id="meme_dreme" name="DREME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="meme_dreme" name="DREME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>- Discriminative Regular Expression Motif Elicitation</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="2.7">python</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 @CHECK_NON_COMMERCIAL_USE@
 dreme
@@ -32,30 +30,23 @@
     #end if
     ]]></command>
     <inputs>
-        <param name="pos_fasta_file" type="data" format="fasta" label="Positive FASTA sequence file" argument="-p"
-               help="positive (primary) sequence file"/>
+        <param name="pos_fasta_file" argument="-p" type="data" format="fasta" label="Positive FASTA sequence file" help="positive (primary) sequence file"/>
         <param name="alphabet_type" type="select" label="Type of sequence alphabet">
             <option value="-dna" selected="true">DNA (default)</option>
             <option value="-rna">RNA</option>
             <option value="-protein">Protein</option>
         </param>
-        <param argument="-norc" label="Check reverse complement" type="boolean"
-               truevalue="" falsevalue="-norc" checked="False"
-               help="Search for motifs also on reverse complement strand"/>
+        <param argument="-norc" type="boolean" truevalue="" falsevalue="-norc" checked="False" label="Check reverse complement" help="Search for motifs also on reverse complement strand"/>
         <conditional name="neg_set_type">
             <param name="neg_set_type_selector" type="select" label="Negative set definition">
                 <option value="shuffle_negs" selected="true">Shuffle positive sequences</option>
                 <option value="supply_negs">Supply negative sequences</option>
             </param>
             <when value="shuffle_negs">
-                <param name="pos_shuffle_seed" type="integer" value="1"
-                       label="Seed for shuffling positive sequences" argument="-s"
-                       help="(default: 1)"/>
+                <param name="pos_shuffle_seed" argument="-s" type="integer" value="1" label="Seed for shuffling positive sequences" help="(default: 1)"/>
             </when>
             <when value="supply_negs">
-                <param name="neg_fasta_file" type="data" format="fasta"
-                       label="Negative FASTA sequence file" argument="-n"
-                       help="negative (control) sequence file (default: positive sequences are shuffled to create the negative set)"/>
+                <param name="neg_fasta_file" argument="-n" type="data" format="fasta" label="Negative FASTA sequence file" help="negative (control) sequence file (default: positive sequences are shuffled to create the negative set)"/>
             </when>
         </conditional>
         <conditional name="options_type">
@@ -63,31 +54,19 @@
                 <option value="basic" selected="true">Basic</option>
                 <option value="advanced">Advanced</option>
             </param>
-            <when value="basic" />
+            <when value="basic"/>
             <when value="advanced">
-                <param name="e_value_thr" type="float" value="0.05"
-                       label="stop if motif E-value > e" argument="-e"
-                       help="stop if motif E-value > given threshold (default: 0.05)">
-                       <validator type="expression" message="Set e-value must be > 0.">value is not None and value > 0</validator>
+                <param name="e_value_thr" argument="-e" type="float" value="0.05" label="stop if motif E-value &gt; e" help="stop if motif E-value &gt; given threshold (default: 0.05)">
+                    <validator type="expression" message="Set e-value must be &gt; 0.">value is not None and value &gt; 0</validator>
                 </param>
-                <param name="motif_min_k" type="integer" value="3" min="1"
-                       label="Minimum width of core motif" argument="-mink"
-                       help="minimum width of core motif (default: 3)"/>
-                <param name="motif_max_k" type="integer" value="8" min="1"
-                       label="Maximum width of core motif" argument="-maxk"
-                       help="maximum width of core motif (default: 8)"/>
-                <param name="stop_m_motifs" type="integer" optional="True" min="1"
-                       label="Stop if m motifs have been output" argument="-m"
-                       help="stop if m motifs have been output (default: only stop at E-value threshold)"/>
-                <param name="stop_t_seconds" type="integer" optional="True" min="1"
-                       label="Stop if the specified time has elapsed" argument="-t"
-                       help="stop if the specified time has elapsed (default: only stop at E-value threshold)"/>
-                <param name="nr_res_generalize" type="integer" value="100" min="1"
-                       label="Number of REs to generalize" argument="-g"
-                       help="number of REs to generalize (default: 100) (Hint: Increasing n will make the motif search more thoroughly at some cost in speed)"/>
+                <param name="motif_min_k" argument="-mink" type="integer" min="1" value="3" label="Minimum width of core motif" help="minimum width of core motif (default: 3)"/>
+                <param name="motif_max_k" argument="-maxk" type="integer" min="1" value="8" label="Maximum width of core motif" help="maximum width of core motif (default: 8)"/>
+                <param name="stop_m_motifs" argument="-m" type="integer" min="1" optional="True" label="Stop if m motifs have been output" help="stop if m motifs have been output (default: only stop at E-value threshold)"/>
+                <param name="stop_t_seconds" argument="-t" type="integer" min="1" optional="True" label="Stop if the specified time has elapsed" help="stop if the specified time has elapsed (default: only stop at E-value threshold)"/>
+                <param name="nr_res_generalize" argument="-g" type="integer" min="1" value="100" label="Number of REs to generalize" help="number of REs to generalize (default: 100) (Hint: Increasing n will make the motif search more thoroughly at some cost in speed)"/>
             </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>
     </inputs>
@@ -102,9 +81,34 @@
             <param name="alphabet_type" value="-rna"/>
             <param name="norc" value="false"/>
             <param name="non_commercial_use" value="True"/>
-            <output name="html_outfile" file="dreme_output_test1.html" compare="contains"/>
-            <output name="txt_outfile" file="dreme_output_test1.txt" compare="contains"/>
-            <output name="xml_outfile" file="dreme_output_test1.xml" compare="contains"/>
+            <output name="html_outfile">
+                <assert_contents>
+                    <has_text text="pvalue"/>
+                    <has_text text="UUUUCC"/>
+                    <has_text text="evalue"/>
+                    <has_text text="matches"/>
+                    <has_text text="DREME"/>
+                </assert_contents>
+            </output>
+            <output name="txt_outfile">
+                <assert_contents>
+                    <has_text text="RNA-LIKE"/>
+                    <has_text text="shuffled"/>
+                    <has_text text="0.221"/>
+                    <has_text text="DREME"/>
+                    <has_text text="letter-probability matrix"/>
+                    <has_n_lines n="84"/>
+                </assert_contents>
+            </output>
+            <output name="xml_outfile">
+                <assert_contents>
+                    <has_text text="Adenine"/>
+                    <has_text text="command_line"/>
+                    <has_text text="Uracil"/>
+                    <has_text text="DREME"/>
+                    <has_text text="evalue"/>
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="pos_fasta_file" value="dreme_test_sites.fa" ftype="fasta"/>
@@ -115,9 +119,35 @@
             <param name="motif_min_k" value="4"/>
             <param name="motif_max_k" value="10"/>
             <param name="non_commercial_use" value="True"/>
-            <output name="html_outfile" file="dreme_output_test2.html" compare="contains"/>
-            <output name="txt_outfile" file="dreme_output_test2.txt" compare="contains"/>
-            <output name="xml_outfile" file="dreme_output_test2.xml" compare="contains"/>
+            <output name="html_outfile">
+                <assert_contents>
+                    <has_text text="shuffled positive sequences"/>
+                    <has_text text="UUCUCU"/>
+                    <has_text text="YAGG"/>
+                    <has_text text="runtime"/>
+                    <has_text text="DREME"/>
+                    <has_text text="ACGU"/>
+                </assert_contents>
+            </output>
+            <output name="txt_outfile">
+                <assert_contents>
+                    <has_text text="RNA-LIKE"/>
+                    <has_text text="from shuffled positives"/>
+                    <has_text text="MOTIF UUYUCY DREME"/>
+                    <has_text text="probability"/>
+                    <has_text text="YAGG"/>
+                    <has_n_lines n="68"/>
+                </assert_contents>
+            </output>
+            <output name="xml_outfile">
+                <assert_contents>
+                    <has_text text="Purine"/>
+                    <has_text text="1000"/>
+                    <has_text text="shuffled"/>
+                    <has_text text="rna"/>
+                    <has_text text="evalue"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
--- a/macros.xml	Sat Apr 09 08:32:58 2022 +0000
+++ b/macros.xml	Thu Aug 29 10:19:55 2024 +0000
@@ -1,7 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <macros>
     <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@TOOL_VERSION@">5.4.1</token>
+    <token name="@TOOL_VERSION@">5.5.6</token>
+    <token name="@PROFILE@">23.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">meme</requirement>
--- a/test-data/dreme_output_test1.html	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-    </div>
-    <div class="box">
-      <h4>Sequences</h4>
-      <table id="seq_info" class="inputs">
-        <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th>
-          <th>Alphabet <div class="help" data-topic="pop_seq_alph"></div></th>
-          <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th>
-        </tr>
-        <tr>
-          <td id="ins_seq_source"></td>
-          <td id="ins_seq_alphabet"></td>
-          <td id="ins_seq_count"></td>
-        </tr>
-      </table>
-      <script>
-      {
-        var db = data.sequence_db;
-        $("ins_seq_source").innerHTML = db.file;
-        $("ins_seq_alphabet").innerHTML = current_alphabet.get_alphabet_name();
-        $("ins_seq_count").innerHTML = db.count;
-      }
-      </script>
-      <h4>Control Sequences</h4>
-      <table id="seq_info" class="inputs">
-        <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th>
-          <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th>
-        </tr>
-        <tr>
-          <td id="ins_cseq_source"></td>
-          <td id="ins_cseq_count"></td>
-        </tr>
-      </table>
-      <script>
-      {
-        var db = data.control_db;
-        if (db.from == "shuffled") {
-          $("ins_cseq_source").innerHTML = "Shuffled Sequences";
-        } else {
-          $("ins_cseq_source").innerHTML = db.file;
-        }
-        $("ins_cseq_count").innerHTML = db.count;
-      }
-      </script>
-      <h4>Background</h4>
-      <span id="alpha_bg"></span>
-      <script>
-      {
-        $("alpha_bg").appendChild(make_alpha_bg_table(current_alphabet, data.control_db.freqs));
-      }
-      </script>
-      <h4>Other Settings</h4>
-      <table id="tbl_settings" class="inputs hide_advanced">
-        <tr>
-          <th>Strand Handling</th>
-          <td id="opt_strand">
-            <span class="strand_none">This alphabet only has one strand</span>
-            <span class="strand_given">Only the given strand is processed</span>
-            <span class="strand_both">Both the given and reverse complement strands are processed</span>
-          </td>
-        </tr>
-        <tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr>
-        <tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr>
-        <tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr>
-        <tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr>
-        <tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr>
-      </table>
-      <script>
-      {
-        $("opt_strand").className = (current_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");
-        $("opt_ngen").innerHTML = data.options.ngen;
-        $("opt_seed").innerHTML = data.options.seed;
-        $("opt_stop_evalue").innerHTML = data.options.stop.evalue;
-        $("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count.");
-        $("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time.");
-      }
-      </script>
-    </div>
-    <!-- list information on this program -->
-    <div id="info_sec" class="bar" style="position:relative">
-      <div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div>
-      <div class="subsection">
-        <h5 id="version">DREME version</h5>
-        <span id="ins_version"></span> 
-        (Release date: <span id="ins_release"></span>)<br>
-      </div>
-      <script>
-        $("ins_version").innerHTML = data["version"];
-        $("ins_release").innerHTML = data["release"];
-      </script>
-      <div class="subsection" id="reference"> <script>print_citation("reference", "DREME");</script> </div>
-      <div class="subsection">
-        <h5 id="command">Command line</h5>
-        <textarea id="cmd" rows="3" style="width:100%;" readonly="readonly">
-        </textarea>
-        <script>$("cmd").value = data["cmd"].join(" ");</script>
-      </div>
-    </div>
-    
-  </body>
-</html>
--- a/test-data/dreme_output_test1.txt	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-MOTIF UUYUCY DREME-1
-
-#             Word        Pos        Neg    P-value    E-value
-# BEST      UUYUCY        387        210   2.6e-018   1.2e-013
-#           UUUUCC        147         75   1.8e-007   8.1e-003
-#           UUUUCU        155         94   2.2e-005   1.0e+000
-#           UUCUCU         94         51   1.3e-004   6.1e+000
-#           UUCUCC         75         42   1.1e-003   5.0e+001
-
-letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 1.2e-013
-0.000000 0.000000 0.000000 1.000000
-0.000000 0.000000 0.000000 1.000000
-0.000000 0.294118 0.000000 0.705882
-0.000000 0.000000 0.000000 1.000000
-0.000000 1.000000 0.000000 0.000000
-0.000000 0.474946 0.000000 0.525054
-
-
-MOTIF YAGG DREME-2
-
-#             Word        Pos        Neg    P-value    E-value
-# BEST        YAGG        600        416   1.1e-016   5.1e-012
-#             CAGG        441        304   1.5e-010   6.6e-006
-#             UAGG        232        165   1.1e-004   4.7e+000
-
-letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 5.1e-012
-0.000000 0.692308 0.000000 0.307692
-1.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 1.000000 0.000000
-0.000000 0.000000 1.000000 0.000000
-
-
-MOTIF GAAGAW DREME-3
-
-#             Word        Pos        Neg    P-value    E-value
-# BEST      GAAGAW         81         22   8.2e-010   3.4e-005
-#           GAAGAU         45          7   2.4e-008   9.9e-004
-#           GAAGAA         40         16   7.9e-004   3.3e+001
-
-letter-probability matrix: alength= 4 w= 6 nsites= 89 E= 3.4e-005
-0.000000 0.000000 1.000000 0.000000
-1.000000 0.000000 0.000000 0.000000
-1.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 1.000000 0.000000
-1.000000 0.000000 0.000000 0.000000
-0.494382 0.000000 0.000000 0.505618
-
-
-MOTIF SMUGGA DREME-4
-
-#             Word        Pos        Neg    P-value    E-value
-# BEST      SMUGGA        110         47   9.1e-008   3.7e-003
-#           GAUGGA         22          6   1.7e-003   7.1e+001
-#           GCUGGA         33         14   3.6e-003   1.5e+002
-#           CCUGGA         32         15   8.6e-003   3.5e+002
-#           CAUGGA         29         13   9.1e-003   3.7e+002
-
-letter-probability matrix: alength= 4 w= 6 nsites= 119 E= 3.7e-003
-0.000000 0.529412 0.470588 0.000000
-0.428571 0.571429 0.000000 0.000000
-0.000000 0.000000 0.000000 1.000000
-0.000000 0.000000 1.000000 0.000000
-0.000000 0.000000 1.000000 0.000000
-1.000000 0.000000 0.000000 0.000000
--- a/test-data/dreme_output_test1.xml	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,44 +0,0 @@
-  <motifs>
-    <motif id="m01" alt="DREME-1" seq="UUYUCY" length="6" nsites="459" p="387" n="210" pvalue="2.6e-018" evalue="1.2e-013" unerased_evalue="1.2e-013">
-      <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
-      <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
-      <pos A="0.000000" C="0.294118" G="0.000000" U="0.705882"/>
-      <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
-      <pos A="0.000000" C="1.000000" G="0.000000" U="0.000000"/>
-      <pos A="0.000000" C="0.474946" G="0.000000" U="0.525054"/>
-      <match seq="UUUUCC" p="147" n="75" pvalue="1.8e-007" evalue="8.1e-003"/>
-      <match seq="UUUUCU" p="155" n="94" pvalue="2.2e-005" evalue="1.0e+000"/>
-      <match seq="UUCUCU" p="94" n="51" pvalue="1.3e-004" evalue="6.1e+000"/>
-      <match seq="UUCUCC" p="75" n="42" pvalue="1.1e-003" evalue="5.0e+001"/>
-    </motif>
-    <motif id="m02" alt="DREME-2" seq="YAGG" length="4" nsites="793" p="600" n="416" pvalue="1.1e-016" evalue="5.1e-012" unerased_evalue="2.4e-012">
-      <pos A="0.000000" C="0.692308" G="0.000000" U="0.307692"/>
-      <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
-      <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
-      <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
-      <match seq="CAGG" p="441" n="304" pvalue="1.5e-010" evalue="6.6e-006"/>
-      <match seq="UAGG" p="232" n="165" pvalue="1.1e-004" evalue="4.7e+000"/>
-    </motif>
-    <motif id="m03" alt="DREME-3" seq="GAAGAW" length="6" nsites="89" p="81" n="22" pvalue="8.2e-010" evalue="3.4e-005" unerased_evalue="3.5e-004">
-      <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
-      <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
-      <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
-      <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
-      <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
-      <pos A="0.494382" C="0.000000" G="0.000000" U="0.505618"/>
-      <match seq="GAAGAU" p="45" n="7" pvalue="2.4e-008" evalue="9.9e-004"/>
-      <match seq="GAAGAA" p="40" n="16" pvalue="7.9e-004" evalue="3.3e+001"/>
-    </motif>
-    <motif id="m04" alt="DREME-4" seq="SMUGGA" length="6" nsites="119" p="110" n="47" pvalue="9.1e-008" evalue="3.7e-003" unerased_evalue="2.6e-005">
-      <pos A="0.000000" C="0.529412" G="0.470588" U="0.000000"/>
-      <pos A="0.428571" C="0.571429" G="0.000000" U="0.000000"/>
-      <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
-      <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
-      <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
-      <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
-      <match seq="GAUGGA" p="22" n="6" pvalue="1.7e-003" evalue="7.1e+001"/>
-      <match seq="GCUGGA" p="33" n="14" pvalue="3.6e-003" evalue="1.5e+002"/>
-      <match seq="CCUGGA" p="32" n="15" pvalue="8.6e-003" evalue="3.5e+002"/>
-      <match seq="CAUGGA" p="29" n="13" pvalue="9.1e-003" evalue="3.7e+002"/>
-    </motif>
-  </motifs>
\ No newline at end of file
--- a/test-data/dreme_output_test2.html	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-      <h4>Other Settings</h4>
-      <table id="tbl_settings" class="inputs hide_advanced">
-        <tr>
-          <th>Strand Handling</th>
-          <td id="opt_strand">
-            <span class="strand_none">This alphabet only has one strand</span>
-            <span class="strand_given">Only the given strand is processed</span>
-            <span class="strand_both">Both the given and reverse complement strands are processed</span>
-          </td>
-        </tr>
-        <tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr>
-        <tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr>
-        <tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr>
-        <tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr>
-        <tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr>
-      </table>
-      <script>
-      {
-        $("opt_strand").className = (current_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");
-        $("opt_ngen").innerHTML = data.options.ngen;
-        $("opt_seed").innerHTML = data.options.seed;
-        $("opt_stop_evalue").innerHTML = data.options.stop.evalue;
-        $("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count.");
-        $("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time.");
-      }
-      </script>
-    </div>
-    <!-- list information on this program -->
-    <div id="info_sec" class="bar" style="position:relative">
-      <div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div>
-      <div class="subsection">
-        <h5 id="version">DREME version</h5>
-        <span id="ins_version"></span> 
-        (Release date: <span id="ins_release"></span>)<br>
-      </div>
-      <script>
-        $("ins_version").innerHTML = data["version"];
-        $("ins_release").innerHTML = data["release"];
-      </script>
-      <div class="subsection" id="reference"> <script>print_citation("reference", "DREME");</script> </div>
-      <div class="subsection">
-        <h5 id="command">Command line</h5>
-        <textarea id="cmd" rows="3" style="width:100%;" readonly="readonly">
-        </textarea>
-        <script>$("cmd").value = data["cmd"].join(" ");</script>
-      </div>
-    </div>
-    
-  </body>
-</html>
--- a/test-data/dreme_output_test2.txt	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,55 +0,0 @@
-ALPHABET "RNA" RNA-LIKE
-A "Adenine" CC0000
-C "Cytosine" 0000CC
-G "Guanine" FFB300
-U "Uracil" 008000
-N "Any base" = ACGU
-X = ACGU
-. = ACGU
-V "Not U" = ACG
-H "Not G" = ACU
-D "Not C" = AGU
-B "Not A" = CGU
-M "Amino" = AC
-R "Purine" = AG
-W "Weak" = AU
-S "Strong" = CG
-Y "Pyrimidine" = CU
-K "Keto" = GU
-T = U
-END ALPHABET
-
-Background letter frequencies (from dataset):
-A 0.221 C 0.245 G 0.221 U 0.312
-
-
-MOTIF UUYUCY DREME-1
-
-#             Word        Pos        Neg    P-value    E-value
-# BEST      UUYUCY        387        210   2.6e-018   3.3e-013
-#           UUUUCC        147         75   1.8e-007   2.2e-002
-#           UUUUCU        155         94   2.2e-005   2.8e+000
-#           UUCUCU         94         51   1.3e-004   1.7e+001
-#           UUCUCC         75         42   1.1e-003   1.4e+002
-
-letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 3.3e-013
-0.000000 0.000000 0.000000 1.000000
-0.000000 0.000000 0.000000 1.000000
-0.000000 0.294118 0.000000 0.705882
-0.000000 0.000000 0.000000 1.000000
-0.000000 1.000000 0.000000 0.000000
-0.000000 0.474946 0.000000 0.525054
-
-
-MOTIF YAGG DREME-2
-
-#             Word        Pos        Neg    P-value    E-value
-# BEST        YAGG        600        416   1.1e-016   1.4e-011
-#             CAGG        441        304   1.5e-010   1.8e-005
-#             UAGG        232        165   1.1e-004   1.3e+001
-
-letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 1.4e-011
-0.000000 0.692308 0.000000 0.307692
-1.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 1.000000 0.000000
-0.000000 0.000000 1.000000 0.000000
\ No newline at end of file
--- a/test-data/dreme_output_test2.xml	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-  <motifs>
-    <motif id="m01" alt="DREME-1" seq="UUYUCY" length="6" nsites="459" p="387" n="210" pvalue="2.6e-018" evalue="3.3e-013" unerased_evalue="3.3e-013">
-      <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
-      <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
-      <pos A="0.000000" C="0.294118" G="0.000000" U="0.705882"/>
-      <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
-      <pos A="0.000000" C="1.000000" G="0.000000" U="0.000000"/>
-      <pos A="0.000000" C="0.474946" G="0.000000" U="0.525054"/>
-      <match seq="UUUUCC" p="147" n="75" pvalue="1.8e-007" evalue="2.2e-002"/>
-      <match seq="UUUUCU" p="155" n="94" pvalue="2.2e-005" evalue="2.8e+000"/>
-      <match seq="UUCUCU" p="94" n="51" pvalue="1.3e-004" evalue="1.7e+001"/>
-      <match seq="UUCUCC" p="75" n="42" pvalue="1.1e-003" evalue="1.4e+002"/>
-    </motif>
-    <motif id="m02" alt="DREME-2" seq="YAGG" length="4" nsites="793" p="600" n="416" pvalue="1.1e-016" evalue="1.4e-011" unerased_evalue="6.3e-012">
-      <pos A="0.000000" C="0.692308" G="0.000000" U="0.307692"/>
-      <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
-      <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
-      <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
-      <match seq="CAGG" p="441" n="304" pvalue="1.5e-010" evalue="1.8e-005"/>
-      <match seq="UAGG" p="232" n="165" pvalue="1.1e-004" evalue="1.3e+001"/>
-    </motif>
-  </motifs>
\ No newline at end of file
--- a/test-data/fimo_output_test1.gff	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-##gff-version 3
-chrM	fimo	nucleotide_motif	6529	6536	46.6	+	.	Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-1-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA;
-chrM	fimo	nucleotide_motif	7741	7748	46.6	+	.	Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-2-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA;
-chrM	fimo	nucleotide_motif	13656	13663	46.6	+	.	Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-3-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA;
-chrM	fimo	nucleotide_motif	13740	13747	46.6	+	.	Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-4-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA;
-chrM	fimo	nucleotide_motif	2299	2306	46.6	-	.	Name=TACTAAYM_chrM-;Alias=MEME-1;ID=TACTAAYM-MEME-1-5-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA;
-chrM	fimo	nucleotide_motif	861	868	 44	+	.	Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-6-chrM;pvalue=3.96e-05;qvalue=0.185;sequence=TACTAACC;
-chrM	fimo	nucleotide_motif	9346	9353	 44	+	.	Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-7-chrM;pvalue=3.96e-05;qvalue=0.185;sequence=TACTAACC;
-chrM	fimo	nucleotide_motif	3767	3774	41.8	+	.	Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-8-chrM;pvalue=6.62e-05;qvalue=0.216;sequence=TACTAATA;
-chrM	fimo	nucleotide_motif	5497	5504	41.8	+	.	Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-9-chrM;pvalue=6.62e-05;qvalue=0.216;sequence=TACTAATA;
-chrM	fimo	nucleotide_motif	10105	10112	41.8	+	.	Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-10-chrM;pvalue=6.62e-05;qvalue=0.216;sequence=TACTAATA;
-chrM	fimo	nucleotide_motif	10959	10966	40.6	+	.	Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-11-chrM;pvalue=8.79e-05;qvalue=0.261;sequence=TACTAACT;
--- a/test-data/fimo_output_test1.html	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-    <td style="padding-right: 2em">background file name = --nrdb--</td>
-    <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td>
-    <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td>
-  </tr>  <tr>
-    <td style="padding-right: 2em">allow clobber = false</td>
-    <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td>
-    <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td>
-  </tr>
-  <tr>
-    <td style="padding-right: 2em">text only = false</td>
-    <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>
-    <td style="padding-left: 5em; padding-right: 2em">max strand = false</td>
-  </tr>
-  <tr>
-    <td style="padding-right: 2em">threshold type = p-value</td>
-    <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.0001</td>
-    <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
-  </tr>
-  <tr>
-    <td style="padding-right: 2em">alpha = 1</td>
-    <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td>
-    <td style="padding-left: 5em; padding-right: 2em"></td>
-  </tr>
-
-</table>
-</pre>
-<p>
-This information can be useful in the event you wish to report a
-problem with the FIMO software.
-</p>
-<hr>
-<span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>
-</body>
-</html>
--- a/test-data/fimo_output_test1.txt	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-motif_id	motif_alt_id	sequence_name	start	stop	strand	score	p-value	q-value	matched_sequence
-TACTAAYM	MEME-1	chrM	6529	6536	+	12.9701	2.18e-05	0.142	TACTAACA
-TACTAAYM	MEME-1	chrM	7741	7748	+	12.9701	2.18e-05	0.142	TACTAACA
-TACTAAYM	MEME-1	chrM	13656	13663	+	12.9701	2.18e-05	0.142	TACTAACA
-TACTAAYM	MEME-1	chrM	13740	13747	+	12.9701	2.18e-05	0.142	TACTAACA
-TACTAAYM	MEME-1	chrM	2299	2306	-	12.9701	2.18e-05	0.142	TACTAACA
-TACTAAYM	MEME-1	chrM	861	868	+	12.2836	3.96e-05	0.185	TACTAACC
-TACTAAYM	MEME-1	chrM	9346	9353	+	12.2836	3.96e-05	0.185	TACTAACC
-TACTAAYM	MEME-1	chrM	3767	3774	+	11.7164	6.62e-05	0.216	TACTAATA
-TACTAAYM	MEME-1	chrM	5497	5504	+	11.7164	6.62e-05	0.216	TACTAATA
-TACTAAYM	MEME-1	chrM	10105	10112	+	11.7164	6.62e-05	0.216	TACTAATA
-TACTAAYM	MEME-1	chrM	10959	10966	+	11.6567	8.79e-05	0.261	TACTAACT
--- a/test-data/fimo_output_test1.xml	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-<setting name="background file name">--nrdb--</setting>
-<setting name="allow clobber">false</setting>
-<setting name="compute q-values">true</setting>
-<setting name="parse genomic coord.">false</setting>
-<setting name="text only">false</setting>
-<setting name="scan both strands">true</setting>
-<setting name="output threshold">0.0001</setting>
-<setting name="threshold type">p-value</setting>
-<setting name="max stored scores">100000</setting>
-<setting name="pseudocount">0.1</setting>
-<setting name="verbosity">2</setting>
-</settings>
-<sequence-data num-sequences="1" num-residues="16569" />
-<alphabet name="DNA" like="dna">
-<letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
-<letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/>
-<letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/>
-<letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/>
-<letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/>
-<letter id="V" symbol="V" equals="ACG" name="Not T"/>
-<letter id="H" symbol="H" equals="ACT" name="Not G"/>
-<letter id="D" symbol="D" equals="AGT" name="Not C"/>
-<letter id="B" symbol="B" equals="CGT" name="Not A"/>
-<letter id="M" symbol="M" equals="AC" name="Amino"/>
-<letter id="R" symbol="R" equals="AG" name="Purine"/>
-<letter id="W" symbol="W" equals="AT" name="Weak"/>
-<letter id="S" symbol="S" equals="CG" name="Strong"/>
-<letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/>
-<letter id="K" symbol="K" equals="GT" name="Keto"/>
-</alphabet>
-<motif name="TACTAAYM" alt="MEME-1" width="8" best-possible-match="TACTAACA"/>
-<background source="--nrdb--">
-<value letter="A">0.275</value>
-<value letter="C">0.225</value>
-<value letter="G">0.225</value>
-<value letter="T">0.275</value>
-</background>
-<cisml-file>cisml.xml</cisml-file>
-</fimo>
--- a/test-data/fimo_output_test2.gff	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-##gff-version 3
-chrM	fimo	nucleotide_motif	440	446	40.9	+	.	Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-1-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA;
-chrM	fimo	nucleotide_motif	2093	2099	40.9	-	.	Name=ACTAAYH_chrM-;Alias=DREME-1;ID=ACTAAYH-DREME-1-2-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA;
-chrM	fimo	nucleotide_motif	2299	2305	40.9	-	.	Name=ACTAAYH_chrM-;Alias=DREME-1;ID=ACTAAYH-DREME-1-3-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA;
-chrM	fimo	nucleotide_motif	5186	5192	40.9	+	.	Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-4-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA;
-chrM	fimo	nucleotide_motif	6530	6536	40.9	+	.	Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-5-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA;
-chrM	fimo	nucleotide_motif	7742	7748	40.9	+	.	Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-6-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA;
-chrM	fimo	nucleotide_motif	13657	13663	40.9	+	.	Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-7-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA;
-chrM	fimo	nucleotide_motif	13741	13747	40.9	+	.	Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-8-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA;
-chrM	fimo	nucleotide_motif	510	516	43.8	+	.	Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-1-chrM;pvalue=4.15e-05;qvalue=0.683;sequence=CCAGCAC;
-chrM	fimo	nucleotide_motif	5137	5143	43.8	+	.	Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-2-chrM;pvalue=4.15e-05;qvalue=0.683;sequence=CCAGCAC;
-chrM	fimo	nucleotide_motif	4241	4247	40.3	+	.	Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-3-chrM;pvalue=9.37e-05;qvalue=1;sequence=CCAGCAT;
--- a/test-data/fimo_output_test2.html	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-    <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td>
-    <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td>
-  </tr>  <tr>
-    <td style="padding-right: 2em">allow clobber = false</td>
-    <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td>
-    <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td>
-  </tr>
-  <tr>
-    <td style="padding-right: 2em">text only = false</td>
-    <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>
-    <td style="padding-left: 5em; padding-right: 2em">max strand = false</td>
-  </tr>
-  <tr>
-    <td style="padding-right: 2em">threshold type = p-value</td>
-    <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.0001</td>
-    <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
-  </tr>
-  <tr>
-    <td style="padding-right: 2em">alpha = 1</td>
-    <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td>
-    <td style="padding-left: 5em; padding-right: 2em"></td>
-  </tr>
-
-</table>
-</pre>
-<p>
-This information can be useful in the event you wish to report a
-problem with the FIMO software.
-</p>
-<hr>
-<span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>
-</body>
-</html>
--- a/test-data/fimo_output_test2.txt	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-motif_id	motif_alt_id	sequence_name	start	stop	strand	score	p-value	q-value	matched_sequence
-CCAGCAY	DREME-5	chrM	510	516	+	13.5843	4.15e-05	0.683	CCAGCAC
-CCAGCAY	DREME-5	chrM	5137	5143	+	13.5843	4.15e-05	0.683	CCAGCAC
-ACTAAYH	DREME-1	chrM	440	446	+	11.7286	8.2e-05	0.332	ACTAACA
-ACTAAYH	DREME-1	chrM	2093	2099	-	11.7286	8.2e-05	0.332	ACTAACA
-ACTAAYH	DREME-1	chrM	2299	2305	-	11.7286	8.2e-05	0.332	ACTAACA
-ACTAAYH	DREME-1	chrM	5186	5192	+	11.7286	8.2e-05	0.332	ACTAACA
-ACTAAYH	DREME-1	chrM	6530	6536	+	11.7286	8.2e-05	0.332	ACTAACA
-ACTAAYH	DREME-1	chrM	7742	7748	+	11.7286	8.2e-05	0.332	ACTAACA
-ACTAAYH	DREME-1	chrM	13657	13663	+	11.7286	8.2e-05	0.332	ACTAACA
-ACTAAYH	DREME-1	chrM	13741	13747	+	11.7286	8.2e-05	0.332	ACTAACA
-CCAGCAY	DREME-5	chrM	4241	4247	+	13.1461	9.37e-05	1	CCAGCAT
\ No newline at end of file
--- a/test-data/fimo_output_test2.xml	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-<setting name="compute q-values">true</setting>
-<setting name="parse genomic coord.">false</setting>
-<setting name="text only">false</setting>
-<setting name="scan both strands">true</setting>
-<setting name="output threshold">0.0001</setting>
-<setting name="threshold type">p-value</setting>
-<setting name="max stored scores">100000</setting>
-<setting name="pseudocount">0.1</setting>
-<setting name="verbosity">2</setting>
-</settings>
-<sequence-data num-sequences="1" num-residues="16569" />
-<alphabet name="DNA" like="dna">
-<letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
-<letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/>
-<letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/>
-<letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/>
-<letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/>
-<letter id="V" symbol="V" equals="ACG" name="Not T"/>
-<letter id="H" symbol="H" equals="ACT" name="Not G"/>
-<letter id="D" symbol="D" equals="AGT" name="Not C"/>
-<letter id="B" symbol="B" equals="CGT" name="Not A"/>
-<letter id="M" symbol="M" equals="AC" name="Amino"/>
-<letter id="R" symbol="R" equals="AG" name="Purine"/>
-<letter id="W" symbol="W" equals="AT" name="Weak"/>
-<letter id="S" symbol="S" equals="CG" name="Strong"/>
-<letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/>
-<letter id="K" symbol="K" equals="GT" name="Keto"/>
-</alphabet>
-<motif name="ACTAAYH" alt="DREME-1" width="7" best-possible-match="ACTAACA"/>
-<motif name="YTAACA" alt="DREME-2" width="6" best-possible-match="TTAACA"/>
-<motif name="TCTGT" alt="DREME-3" width="5" best-possible-match="TCTGT"/>
-<motif name="SCCAGG" alt="DREME-4" width="6" best-possible-match="CCCAGG"/>
-<motif name="CCAGCAY" alt="DREME-5" width="7" best-possible-match="CCAGCAC"/>
-<motif name="GMATGT" alt="DREME-6" width="6" best-possible-match="GAATGT"/>
\ No newline at end of file
--- a/test-data/fimo_output_test3.html	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-    <td style="padding-right: 2em">background file name = --uniform--</td>
-    <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td>
-    <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td>
-  </tr>  <tr>
-    <td style="padding-right: 2em">allow clobber = false</td>
-    <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td>
-    <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td>
-  </tr>
-  <tr>
-    <td style="padding-right: 2em">text only = false</td>
-    <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>
-    <td style="padding-left: 5em; padding-right: 2em">max strand = false</td>
-  </tr>
-  <tr>
-    <td style="padding-right: 2em">threshold type = p-value</td>
-    <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.01</td>
-    <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
-  </tr>
-  <tr>
-    <td style="padding-right: 2em">alpha = 1</td>
-    <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td>
-    <td style="padding-left: 5em; padding-right: 2em"></td>
-  </tr>
\ No newline at end of file
--- a/test-data/fimo_output_test3.txt	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-motif_id	motif_alt_id	sequence_name	start	stop	strand	score	p-value	q-value	matched_sequence
-ACTAAYH	DREME-1	chrM	440	446	+	12.1831	6.1e-05	0.239	ACTAACA
-ACTAAYH	DREME-1	chrM	2093	2099	-	12.1831	6.1e-05	0.239	ACTAACA
-ACTAAYH	DREME-1	chrM	2299	2305	-	12.1831	6.1e-05	0.239	ACTAACA
-ACTAAYH	DREME-1	chrM	5186	5192	+	12.1831	6.1e-05	0.239	ACTAACA
-ACTAAYH	DREME-1	chrM	6530	6536	+	12.1831	6.1e-05	0.239	ACTAACA
-ACTAAYH	DREME-1	chrM	7742	7748	+	12.1831	6.1e-05	0.239	ACTAACA
-ACTAAYH	DREME-1	chrM	13657	13663	+	12.1831	6.1e-05	0.239	ACTAACA
-ACTAAYH	DREME-1	chrM	13741	13747	+	12.1831	6.1e-05	0.239	ACTAACA
-ACTAAYH	DREME-1	chrM	3768	3774	+	11.5915	0.000122	0.239	ACTAATA
-ACTAAYH	DREME-1	chrM	5498	5504	+	11.5915	0.000122	0.239	ACTAATA
-ACTAAYH	DREME-1	chrM	7736	7742	+	11.5915	0.000122	0.239	ACTAATA
-ACTAAYH	DREME-1	chrM	9872	9878	+	11.5915	0.000122	0.239	ACTAATA
-ACTAAYH	DREME-1	chrM	10106	10112	+	11.5915	0.000122	0.239	ACTAATA
-ACTAAYH	DREME-1	chrM	10313	10319	+	11.5915	0.000122	0.239	ACTAATA
-ACTAAYH	DREME-1	chrM	11818	11824	+	11.5915	0.000122	0.239	ACTAATA
-ACTAAYH	DREME-1	chrM	15903	15909	+	11.5915	0.000122	0.239	ACTAATA
-ACTAAYH	DREME-1	chrM	7732	7738	+	11.4507	0.000183	0.294	ACTAACT
-ACTAAYH	DREME-1	chrM	10960	10966	+	11.4507	0.000183	0.294	ACTAACT
-ACTAAYH	DREME-1	chrM	862	868	+	11.2394	0.000244	0.294	ACTAACC
-ACTAAYH	DREME-1	chrM	1832	1838	+	11.2394	0.000244	0.294	ACTAACC
-ACTAAYH	DREME-1	chrM	8679	8685	+	11.2394	0.000244	0.294	ACTAACC
-ACTAAYH	DREME-1	chrM	8770	8776	+	11.2394	0.000244	0.294	ACTAACC
-ACTAAYH	DREME-1	chrM	9347	9353	+	11.2394	0.000244	0.294	ACTAACC
-ACTAAYH	DREME-1	chrM	9359	9365	+	11.2394	0.000244	0.294	ACTAACC
-ACTAAYH	DREME-1	chrM	10302	10308	+	11.2394	0.000244	0.294	ACTAACC
-ACTAAYH	DREME-1	chrM	14765	14771	+	11.2394	0.000244	0.294	ACTAACC
-ACTAAYH	DREME-1	chrM	4466	4472	+	10.8592	0.000305	0.302	ACTAATT
-ACTAAYH	DREME-1	chrM	11248	11254	+	10.8592	0.000305	0.302	ACTAATT
-ACTAAYH	DREME-1	chrM	475	481	+	10.6479	0.000366	0.302	ACTAATC
-ACTAAYH	DREME-1	chrM	7930	7936	+	10.6479	0.000366	0.302	ACTAATC
-ACTAAYH	DREME-1	chrM	8649	8655	+	10.6479	0.000366	0.302	ACTAATC
-ACTAAYH	DREME-1	chrM	8670	8676	+	10.6479	0.000366	0.302	ACTAATC
-ACTAAYH	DREME-1	chrM	10768	10774	+	10.6479	0.000366	0.302	ACTAATC
-ACTAAYH	DREME-1	chrM	11053	11059	+	10.6479	0.000366	0.302	ACTAATC
-ACTAAYH	DREME-1	chrM	11101	11107	+	10.6479	0.000366	0.302	ACTAATC
-ACTAAYH	DREME-1	chrM	12720	12726	+	10.6479	0.000366	0.302	ACTAATC
-ACTAAYH	DREME-1	chrM	13149	13155	+	10.6479	0.000366	0.302	ACTAATC
-ACTAAYH	DREME-1	chrM	14216	14222	+	10.6479	0.000366	0.302	ACTAATC
-ACTAAYH	DREME-1	chrM	678	684	-	-1.07042	0.000549	0.366	ACTAAGA
\ No newline at end of file
--- a/test-data/fimo_output_test3.xml	Sat Apr 09 08:32:58 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-<sequence-data num-sequences="1" num-residues="16569" />
-<alphabet name="DNA" like="dna">
-<letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
-<letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/>
-<letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/>
-<letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/>
-<letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/>
-<letter id="V" symbol="V" equals="ACG" name="Not T"/>
-<letter id="H" symbol="H" equals="ACT" name="Not G"/>
-<letter id="D" symbol="D" equals="AGT" name="Not C"/>
-<letter id="B" symbol="B" equals="CGT" name="Not A"/>
-<letter id="M" symbol="M" equals="AC" name="Amino"/>
-<letter id="R" symbol="R" equals="AG" name="Purine"/>
-<letter id="W" symbol="W" equals="AT" name="Weak"/>
-<letter id="S" symbol="S" equals="CG" name="Strong"/>
-<letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/>
-<letter id="K" symbol="K" equals="GT" name="Keto"/>
-</alphabet>
-<motif name="ACTAAYH" alt="DREME-1" width="7" best-possible-match="ACTAACA"/>
-<motif name="YTAACA" alt="DREME-2" width="6" best-possible-match="TTAACA"/>
-<motif name="TCTGT" alt="DREME-3" width="5" best-possible-match="TCTGT"/>
-<motif name="SCCAGG" alt="DREME-4" width="6" best-possible-match="CCCAGG"/>
-<motif name="CCAGCAY" alt="DREME-5" width="7" best-possible-match="CCAGCAC"/>
-<motif name="GMATGT" alt="DREME-6" width="6" best-possible-match="GAATGT"/>
-<background source="--uniform--">
-<value letter="A">0.250</value>
-<value letter="C">0.250</value>
-<value letter="G">0.250</value>
-<value letter="T">0.250</value>
-</background>
-<cisml-file>cisml.xml</cisml-file>
-</fimo>