Repository 'meme_fimo'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo

Changeset 18:c5209f38700d (2022-04-09)
Previous changeset 17:d7a6ea1e3b9d (2021-11-27) Next changeset 19:01f5d04846c4 (2024-08-29)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
modified:
fimo.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.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
test-data/meme_output_test1.html
test-data/meme_output_test1.txt
test-data/meme_output_test1.xml
test-data/meme_output_test2.html
test-data/meme_output_test2.txt
test-data/meme_output_test2.xml
b
diff -r d7a6ea1e3b9d -r c5209f38700d fimo.xml
--- a/fimo.xml Sat Nov 27 14:37:42 2021 +0000
+++ b/fimo.xml Sat Apr 09 08:32:23 2022 +0000
b
@@ -1,4 +1,4 @@
-<tool id="meme_fimo" name="FIMO" version="@TOOL_VERSION@.0">
+<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>
b
diff -r d7a6ea1e3b9d -r c5209f38700d macros.xml
--- a/macros.xml Sat Nov 27 14:37:42 2021 +0000
+++ b/macros.xml Sat Apr 09 08:32:23 2022 +0000
b
@@ -1,9 +1,10 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <macros>
-    <token name="@TOOL_VERSION@">5.0.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@TOOL_VERSION@">5.4.1</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="5.0.5">meme</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">meme</requirement>
             <yield/>
         </requirements>
     </xml>
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/dreme_output_test1.html
--- a/test-data/dreme_output_test1.html Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/dreme_output_test1.html Sat Apr 09 08:32:23 2022 +0000
[
b'@@ -1,113 +1,100 @@\n-<!DOCTYPE HTML>\n-<html>\n-  <head>\n-    <meta charset="UTF-8">\n-    <title>DREME</title>\n-    <script>\n-      // @JSON_VAR data\n-      var data = {\n-        "program": "dreme",\n-        "version": "5.0.5",\n-        "cmd": [\n-          "dreme", "-o", "./dreme_out", "-p",\n-          "-norc", "-rna", "-s", "1"\n-        ],\n-        "options": {\n-          "revcomp": false,\n-          "ngen": 100,\n-          "add_pv_thresh": 0.01,\n-          "seed": 1,\n-          "stop": {\n-            "evalue": "0.05"\n-        "alphabet": {\n-          "name": "RNA",\n-          "like": "rna",\n-          "ncore": 4,\n-          "symbols": [\n-        "background": {\n-          "freqs": [0.221, 0.245, 0.221, 0.312]\n-        "control_db": {\n-          "name": "shuffled positive sequences",\n-          "from": "shuffled",\n-          "count": 1000,\n-          "freqs": [0.221, 0.245, 0.221, 0.312]\n-        "motifs": [\n-            "db": 0,\n-            "id": "UUYUCY",\n-            "alt": "DREME-1",\n-            "len": 6,\n-            "nsites": 459,\n-            "evalue": "1.2e-013",\n-            "p": 387,\n-            "n": 210,\n-            "pvalue": "2.6e-018",\n-            "unerased_evalue": "1.2e-013",\n-            "pwm": [\n-              [0.000000, 0.000000, 0.000000, 1.000000], \n-              [0.000000, 0.000000, 0.000000, 1.000000], \n-              [0.000000, 0.294118, 0.000000, 0.705882], \n-              [0.000000, 0.000000, 0.000000, 1.000000], \n-              [0.000000, 1.000000, 0.000000, 0.000000], \n-              [0.000000, 0.474946, 0.000000, 0.525054]\n-            "matches": [\n-                "seq": "UUUUCC",\n-                "p": 147,\n-                "n": 75,\n-                "pvalue": "1.8e-007",\n-                "evalue": "8.1e-003"\n-              }, {\n-                "seq": "UUUUCU",\n-                "p": 155,\n-                "n": 94,\n-                "pvalue": "2.2e-005",\n-                "evalue": "1.0e+000"\n-                "seq": "UUCUCU",\n-                "p": 94,\n-                "n": 51,\n-                "pvalue": "1.3e-004",\n-                "evalue": "6.1e+000"\n-                "seq": "UUCUCC",\n-                "p": 75,\n-                "n": 42,\n-                "pvalue": "1.1e-003",\n-                "evalue": "5.0e+001"\n-    <script>\n-var site_url = "http://meme-suite.org";\n-</script>\n-/* dreme output specific css */\n-/* program settings */\n-</style>\n-  </head>\n-  <body data-scrollpad="true">\n-        The name of the motif uses the IUPAC codes for nucleotides which has \n-        a different letter to represent each of the 15 possible combinations.\n-        The name is itself a representation of the motif though the position\n-        weight matrix is not directly equivalent as it is generated from the\n-        sites found that matched the letters given in the name.\n-      <p>The E-value is the enrichment p-value times the number of candidate \n-        motifs tested.</p>\n-      <p>The enrichment p-value is calculated using Fisher\'s Exact Test for \n-        enrichment of the motif in the positive sequences.</p>\n-      <p>Note that the counts used in Fisher\'s Exact Test are made after \n-        erasing sites that match previously found motifs.</p>\n-      <p>The E-value of the motif calculated without erasing the sites of \n-        previously found motifs.</p>\n-      <p>Show more information on the motif.</p>\n-      <p>Submit your motif to another MEME Suite program or download your motif.</p>\n-      <h5>Supported Programs</h5>\n-        <dt>Tomtom</dt>\n-        <dd>Tomtom is a tool for searching for similar known motifs. \n-        <dt>MAST</dt>\n-        <dd>MAST is a tool for searching biological sequence databases for \n-          sequences that contain one or more of a group of known motifs.\n-        <dt>FIMO</dt>\n-        <dd>FIMO is a tool for searching biological sequence databases for \n-          sequences that contain one or more known motifs.\n-        <dt>GOMo</dt>\n-        <dd>GOMo is a tool for ident'..b'          <th>Alphabet <div class="help" data-topic="pop_seq_alph"></div></th>\n+          <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th>\n+        </tr>\n+        <tr>\n+          <td id="ins_seq_source"></td>\n+          <td id="ins_seq_alphabet"></td>\n+          <td id="ins_seq_count"></td>\n+        </tr>\n+      </table>\n+      <script>\n+      {\n+        var db = data.sequence_db;\n+        $("ins_seq_source").innerHTML = db.file;\n+        $("ins_seq_alphabet").innerHTML = current_alphabet.get_alphabet_name();\n+        $("ins_seq_count").innerHTML = db.count;\n+      }\n+      </script>\n+      <h4>Control Sequences</h4>\n+      <table id="seq_info" class="inputs">\n+        <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th>\n+          <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th>\n+        </tr>\n+        <tr>\n+          <td id="ins_cseq_source"></td>\n+          <td id="ins_cseq_count"></td>\n+        </tr>\n+      </table>\n+      <script>\n+      {\n+        var db = data.control_db;\n+        if (db.from == "shuffled") {\n+          $("ins_cseq_source").innerHTML = "Shuffled Sequences";\n+        } else {\n+          $("ins_cseq_source").innerHTML = db.file;\n+        }\n+        $("ins_cseq_count").innerHTML = db.count;\n+      }\n+      </script>\n+      <h4>Background</h4>\n+      <span id="alpha_bg"></span>\n+      <script>\n+      {\n+        $("alpha_bg").appendChild(make_alpha_bg_table(current_alphabet, data.control_db.freqs));\n+      }\n+      </script>\n+      <h4>Other Settings</h4>\n+      <table id="tbl_settings" class="inputs hide_advanced">\n+        <tr>\n+          <th>Strand Handling</th>\n+          <td id="opt_strand">\n+            <span class="strand_none">This alphabet only has one strand</span>\n+            <span class="strand_given">Only the given strand is processed</span>\n+            <span class="strand_both">Both the given and reverse complement strands are processed</span>\n+          </td>\n+        </tr>\n+        <tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr>\n+        <tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr>\n+        <tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr>\n+        <tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr>\n+        <tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr>\n+      </table>\n+      <script>\n+      {\n+        $("opt_strand").className = (current_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");\n+        $("opt_ngen").innerHTML = data.options.ngen;\n+        $("opt_seed").innerHTML = data.options.seed;\n+        $("opt_stop_evalue").innerHTML = data.options.stop.evalue;\n+        $("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count.");\n+        $("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time.");\n+      }\n+      </script>\n+    </div>\n+    <!-- list information on this program -->\n+    <div id="info_sec" class="bar" style="position:relative">\n+      <div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div>\n+      <div class="subsection">\n+        <h5 id="version">DREME version</h5>\n+        <span id="ins_version"></span> \n+        (Release date: <span id="ins_release"></span>)<br>\n+      </div>\n+      <script>\n+        $("ins_version").innerHTML = data["version"];\n+        $("ins_release").innerHTML = data["release"];\n+      </script>\n+      <div class="subsection" id="reference"> <script>print_citation("reference", "DREME");</script> </div>\n+      <div class="subsection">\n+        <h5 id="command">Command line</h5>\n+        <textarea id="cmd" rows="3" style="width:100%;" readonly="readonly">\n+        </textarea>\n+        <script>$("cmd").value = data["cmd"].join(" ");</script>\n+      </div>\n+    </div>\n+    \n   </body>\n </html>\n'
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/dreme_output_test1.txt
--- a/test-data/dreme_output_test1.txt Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/dreme_output_test1.txt Sat Apr 09 08:32:23 2022 +0000
b
@@ -1,36 +1,12 @@
-# DREME 5.0.5
-#   negatives: 1000 from shuffled positives
+MOTIF UUYUCY DREME-1
 
-MEME version 5.0.5
-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   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
@@ -38,21 +14,29 @@
 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
@@ -60,13 +44,17 @@
 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
@@ -74,4 +62,3 @@
 0.000000 0.000000 1.000000 0.000000
 0.000000 0.000000 1.000000 0.000000
 1.000000 0.000000 0.000000 0.000000
-# Stopping reason: E-value threshold exceeded
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/dreme_output_test1.xml
--- a/test-data/dreme_output_test1.xml Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/dreme_output_test1.xml Sat Apr 09 08:32:23 2022 +0000
b
@@ -1,30 +1,3 @@
-<dreme version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700">
-  <model>
-    <negatives name="shuffled positive sequences" count="1000" from="shuffled"/>
-    <alphabet name="RNA" like="rna">
-      <letter id="A" symbol="A" name="Adenine" colour="CC0000"/>
-      <letter id="C" symbol="C" name="Cytosine" colour="0000CC"/>
-      <letter id="G" symbol="G" name="Guanine" colour="FFB300"/>
-      <letter id="U" symbol="U" aliases="T" name="Uracil" colour="008000"/>
-      <letter id="N" symbol="N" aliases="X." equals="ACGU" name="Any base"/>
-      <letter id="V" symbol="V" equals="ACG" name="Not U"/>
-      <letter id="H" symbol="H" equals="ACU" name="Not G"/>
-      <letter id="D" symbol="D" equals="AGU" name="Not C"/>
-      <letter id="B" symbol="B" equals="CGU" 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="AU" name="Weak"/>
-      <letter id="S" symbol="S" equals="CG" name="Strong"/>
-      <letter id="Y" symbol="Y" equals="CU" name="Pyrimidine"/>
-      <letter id="K" symbol="K" equals="GU" name="Keto"/>
-    </alphabet>
-    <strands>none</strands>
-    <background A="0.221" C="0.245" G="0.221" U="0.312" from="dataset"/>
-    <stop evalue="0.05"/>
-    <ngen>100</ngen>
-    <add_pv_thresh>0.01</add_pv_thresh>
-    <seed>1</seed>
-  </model>
   <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"/>
@@ -68,5 +41,4 @@
       <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>
-</dreme>
+  </motifs>
\ No newline at end of file
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/dreme_output_test2.html
--- a/test-data/dreme_output_test2.html Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/dreme_output_test2.html Sat Apr 09 08:32:23 2022 +0000
[
b'@@ -1,167 +1,50 @@\n-<!DOCTYPE HTML>\n-<html>\n-  <head>\n-    <meta charset="UTF-8">\n-    <title>DREME</title>\n-    <script>\n-      // @JSON_VAR data\n-      var data = {\n-        "program": "dreme",\n-        "version": "5.0.5",\n-        "release": "Mon Mar 18 20:12:19 2019 -0700",\n-        "cmd": [\n-          "dreme", "-o", "./dreme_out", "-p",\n-          "-norc", "-rna", "-s", "1", "-e", "1e-05", "-g", "100", "-mink",\n-          "4", "-maxk", "10"\n-        ],\n-        "options": {\n-          "revcomp": false,\n-          "ngen": 100,\n-          "add_pv_thresh": 0.01,\n-          "seed": 1,\n-          "stop": {\n-            "evalue": "1e-05"\n-          }\n-        },\n-        "alphabet": {\n-          "name": "RNA",\n-          "like": "rna",\n-          "ncore": 4,\n-          "symbols": [\n-            {\n-              "symbol": "A",\n-              "name": "Adenine",\n-              "colour": "CC0000"\n-            }, {\n-              "symbol": "C",\n-              "name": "Cytosine",\n-              "colour": "0000CC"\n-              "symbol": "G",\n-              "name": "Guanine",\n-              "colour": "FFB300"\n-              "symbol": "U",\n-              "aliases": "T",\n-              "name": "Uracil",\n-              "colour": "008000"\n-              "symbol": "N",\n-              "aliases": "X.",\n-              "name": "Any base",\n-              "equals": "ACGU"\n-              "symbol": "V",\n-              "name": "Not U",\n-              "equals": "ACG"\n-              "symbol": "H",\n-              "name": "Not G",\n-              "equals": "ACU"\n-              "symbol": "D",\n-              "name": "Not C",\n-              "equals": "AGU"\n-              "symbol": "B",\n-              "name": "Not A",\n-              "equals": "CGU"\n-              "symbol": "M",\n-              "name": "Amino",\n-              "equals": "AC"\n-              "symbol": "R",\n-              "name": "Purine",\n-              "equals": "AG"\n-              "symbol": "W",\n-              "name": "Weak",\n-              "equals": "AU"\n-              "symbol": "S",\n-              "name": "Strong",\n-              "equals": "CG"\n-              "symbol": "Y",\n-              "name": "Pyrimidine",\n-              "equals": "CU"\n-              "symbol": "K",\n-              "name": "Keto",\n-              "equals": "GU"\n-        "background": {\n-          "freqs": [0.221, 0.245, 0.221, 0.312]\n-        "sequence_db": {\n-          "count": 1000\n-        "control_db": {\n-          "name": "shuffled positive sequences",\n-          "from": "shuffled",\n-          "count": 1000,\n-          "freqs": [0.221, 0.245, 0.221, 0.312]\n-        "motifs": [\n-            "db": 0,\n-            "id": "UUYUCY",\n-            "alt": "DREME-1",\n-            "len": 6,\n-            "nsites": 459,\n-            "evalue": "3.3e-013",\n-            "p": 387,\n-            "n": 210,\n-            "pvalue": "2.6e-018",\n-            "unerased_evalue": "3.3e-013",\n-            "pwm": [\n-              [0.000000, 0.000000, 0.000000, 1.000000], \n-              [0.000000, 0.000000, 0.000000, 1.000000], \n-              [0.000000, 0.294118, 0.000000, 0.705882], \n-              [0.000000, 0.000000, 0.000000, 1.000000], \n-              [0.000000, 1.000000, 0.000000, 0.000000], \n-              [0.000000, 0.474946, 0.000000, 0.525054]\n-            "matches": [\n-                "seq": "UUUUCC",\n-                "p": 147,\n-                "n": 75,\n-                "pvalue": "1.8e-007",\n-                "evalue": "2.2e-002"\n-    </script>\n-var site_url = "http://meme-suite.org";\n-//======================================================================\n-// end RasterizedAlphabet\n-//======================================================================\n-//======================================================================\n-// start LogoMetrics object\n-//======================================================================\n- * Initialise and display the download popup.\n-</style>\n-  </head>\n-  <body data-scrollpad="true">\n-    <!'..b'ch previously found motifs.</p>\n-      <p>The E-value of the motif calculated without erasing the sites of \n-        previously found motifs.</p>\n-      <p>Show more information on the motif.</p>\n-      <p>Submit your motif to another MEME Suite program or download your motif.</p>\n-      <h5>Supported Programs</h5>\n-        <dt>Tomtom</dt>\n-        <dd>Tomtom is a tool for searching for similar known motifs. \n-        <dt>MAST</dt>\n-        <dd>MAST is a tool for searching biological sequence databases for \n-          sequences that contain one or more of a group of known motifs.\n-        <dt>FIMO</dt>\n-        <dd>FIMO is a tool for searching biological sequence databases for \n-          sequences that contain one or more known motifs.\n-        <dt>GOMo</dt>\n-        <dd>GOMo is a tool for identifying possible roles (Gene Ontology \n-          terms) for DNA binding motifs.\n-        <dt>SpaMo</dt>\n-        <dd>SpaMo is a tool for inferring possible transcription factor\n-          complexes by finding motifs with enriched spacings.\n-    <!-- Page starts here -->\n-        <h1>DREME</h1>\n-        <h2>Discriminative Regular Expression Motif Elicitation</h2>\n-        For further information on how to interpret these results please access\n-        To get a copy of the MEME software please access \n-        If you use DREME in your research please cite the following paper:<br />\n-          Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011.\n+      <h4>Other Settings</h4>\n+      <table id="tbl_settings" class="inputs hide_advanced">\n+        <tr>\n+          <th>Strand Handling</th>\n+          <td id="opt_strand">\n+            <span class="strand_none">This alphabet only has one strand</span>\n+            <span class="strand_given">Only the given strand is processed</span>\n+            <span class="strand_both">Both the given and reverse complement strands are processed</span>\n+          </td>\n+        </tr>\n+        <tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr>\n+        <tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr>\n+        <tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr>\n+        <tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr>\n+        <tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr>\n+      </table>\n+      <script>\n+      {\n+        $("opt_strand").className = (current_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");\n+        $("opt_ngen").innerHTML = data.options.ngen;\n+        $("opt_seed").innerHTML = data.options.seed;\n+        $("opt_stop_evalue").innerHTML = data.options.stop.evalue;\n+        $("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count.");\n+        $("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time.");\n+      }\n+      </script>\n+    </div>\n+    <!-- list information on this program -->\n+    <div id="info_sec" class="bar" style="position:relative">\n+      <div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div>\n+      <div class="subsection">\n+        <h5 id="version">DREME version</h5>\n+        <span id="ins_version"></span> \n+        (Release date: <span id="ins_release"></span>)<br>\n+      </div>\n+      <script>\n+        $("ins_version").innerHTML = data["version"];\n+        $("ins_release").innerHTML = data["release"];\n+      </script>\n+      <div class="subsection" id="reference"> <script>print_citation("reference", "DREME");</script> </div>\n+      <div class="subsection">\n+        <h5 id="command">Command line</h5>\n+        <textarea id="cmd" rows="3" style="width:100%;" readonly="readonly">\n+        </textarea>\n+        <script>$("cmd").value = data["cmd"].join(" ");</script>\n+      </div>\n+    </div>\n+    \n   </body>\n </html>\n'
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/dreme_output_test2.txt
--- a/test-data/dreme_output_test2.txt Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/dreme_output_test2.txt Sat Apr 09 08:32:23 2022 +0000
b
@@ -1,7 +1,3 @@
-# DREME 5.0.5
-#   negatives: 1000 from shuffled positives
-
-MEME version 5.0.5
 ALPHABET "RNA" RNA-LIKE
 A "Adenine" CC0000
 C "Cytosine" 0000CC
@@ -22,15 +18,20 @@
 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
@@ -38,14 +39,17 @@
 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
-# Stopping reason: E-value threshold exceeded
+0.000000 0.000000 1.000000 0.000000
\ No newline at end of file
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/dreme_output_test2.xml
--- a/test-data/dreme_output_test2.xml Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/dreme_output_test2.xml Sat Apr 09 08:32:23 2022 +0000
b
@@ -1,30 +1,3 @@
-<dreme version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700">
-  <model>
-    <negatives name="shuffled positive sequences" count="1000" from="shuffled"/>
-    <alphabet name="RNA" like="rna">
-      <letter id="A" symbol="A" name="Adenine" colour="CC0000"/>
-      <letter id="C" symbol="C" name="Cytosine" colour="0000CC"/>
-      <letter id="G" symbol="G" name="Guanine" colour="FFB300"/>
-      <letter id="U" symbol="U" aliases="T" name="Uracil" colour="008000"/>
-      <letter id="N" symbol="N" aliases="X." equals="ACGU" name="Any base"/>
-      <letter id="V" symbol="V" equals="ACG" name="Not U"/>
-      <letter id="H" symbol="H" equals="ACU" name="Not G"/>
-      <letter id="D" symbol="D" equals="AGU" name="Not C"/>
-      <letter id="B" symbol="B" equals="CGU" 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="AU" name="Weak"/>
-      <letter id="S" symbol="S" equals="CG" name="Strong"/>
-      <letter id="Y" symbol="Y" equals="CU" name="Pyrimidine"/>
-      <letter id="K" symbol="K" equals="GU" name="Keto"/>
-    </alphabet>
-    <strands>none</strands>
-    <background A="0.221" C="0.245" G="0.221" U="0.312" from="dataset"/>
-    <stop evalue="1e-05"/>
-    <ngen>100</ngen>
-    <add_pv_thresh>0.01</add_pv_thresh>
-    <seed>1</seed>
-  </model>
   <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"/>
@@ -46,5 +19,4 @@
       <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>
-</dreme>
+  </motifs>
\ No newline at end of file
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/fimo_output_test1.gff
--- a/test-data/fimo_output_test1.gff Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/fimo_output_test1.gff Sat Apr 09 08:32:23 2022 +0000
b
@@ -1,12 +1,12 @@
 ##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;
+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;
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/fimo_output_test1.html
--- a/test-data/fimo_output_test1.html Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/fimo_output_test1.html Sat Apr 09 08:32:23 2022 +0000
b
@@ -1,73 +1,34 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html xmlns:cis="http://zlab.bu.edu/schema/cisml" xmlns:fimo="http://noble.gs.washington.edu/schema/cisml" xmlns:mem="http://noble.gs.washington.edu/meme">
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="UTF-8">
-<title>FIMO Results</title>
-<style type="text/css">
-td.left {text-align: left;}
-td.right {text-align: right; padding-right: 1cm;}
-</head>
-<body color="#000000">
-<a name="top_buttons"></a>
-<hr>
-<table summary="buttons" align="left" cellspacing="0">
-<tr>
-<td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>
-<td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>
-<td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>
-<td bgcolor="#FFDD00"><a href="fimo.tsv""><b>Results in TSV Format</b></a></td>
-<td bgcolor="#FFDDFF"><a href="fimo.gff""><b>Results in GFF3 Format</b></a></td>
-</tr>
+    <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>
-<center><big><b>FIMO - Motif search tool</b></big></center>
-FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700)
-For further information on how to interpret these results please access <a href="http://meme-suite.org/doc/fimo-output-format.html">http://meme-suite.org/doc/fimo-output-format.html</a>.<br>
-To get a copy of the FIMO software please access <a href="http://meme-suite.org">http://meme-suite.org</a>
-<p>If you use FIMO in your research, please cite the following paper:<br>
-Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
-"FIMO: Scanning for occurrences of a given motif",
-<i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
-<center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
-  Database contains 1 sequences, 16569 residues
-         BEST POSSIBLE MATCH
-Random model letter frequencies (--nrdb--):
-A 0.275 C 0.225 G 0.225 T 0.275 </p>
-<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
-There were 11 motif occurences with a p-value less than 0.0001.
-The full set of motif occurences can be seen in the
-TSV (tab-delimited values) output file
-The <i>p</i>-value of a motif occurrence is defined as the
-probability of a random sequence of the same length as the motif
-matching that position of the sequence with as good or better a score.
-The score for the match of a position in a sequence to a motif
-is computed by summing the appropriate entries from each column of
-the position-dependent scoring matrix that represents the motif.
-The q-value of a motif occurrence is defined as the
-false discovery rate if the occurrence is accepted as significant.
-<li>The table is sorted by increasing <i>p</i>-value.</li>
-<th>Motif ID</th>
-<th>Alt ID</th>
-<th>Sequence Name</th>
-<th>Strand</th>
-<th>Start</th>
-<th>End</th>
-<th>p-value</th>
-<th>q-value</th>
-<th>Matched Sequence</th>
-      <td style="text-align:left;">TACTAAYM</td>
-      <td style="text-align:left;">MEME-1</td>
-      <td style="text-align:left;">chrM</td>
-      <td style="text-align:center;">+</td>
-      <td style="text-align:left;">6529</td>
-      <td style="text-align:left;">6536</td>
-      <td style="text-align:left;">2.18e-05</td>
-      <td style="text-align:left;">0.142</td>
-      <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td>
-</table>
-<hr>
-<center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
+</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>
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/fimo_output_test1.xml
--- a/test-data/fimo_output_test1.xml Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/fimo_output_test1.xml Sat Apr 09 08:32:23 2022 +0000
b
@@ -1,10 +1,3 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!-- Begin document body -->
-<fimo version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700">
-  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
->
-<settings>
 <setting name="background file name">--nrdb--</setting>
 <setting name="allow clobber">false</setting>
 <setting name="compute q-values">true</setting>
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/fimo_output_test2.gff
--- a/test-data/fimo_output_test2.gff Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/fimo_output_test2.gff Sat Apr 09 08:32:23 2022 +0000
b
@@ -1,12 +1,12 @@
 ##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;
+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;
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/fimo_output_test2.html
--- a/test-data/fimo_output_test2.html Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/fimo_output_test2.html Sat Apr 09 08:32:23 2022 +0000
b
@@ -1,90 +1,33 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html xmlns:cis="http://zlab.bu.edu/schema/cisml" xmlns:fimo="http://noble.gs.washington.edu/schema/cisml" xmlns:mem="http://noble.gs.washington.edu/meme">
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="UTF-8">
-<title>FIMO Results</title>
-<style type="text/css">
-td.left {text-align: left;}
-td.right {text-align: right; padding-right: 1cm;}
-</style>
-</head>
-<body color="#000000">
-<a name="top_buttons"></a>
-<hr>
-<table summary="buttons" align="left" cellspacing="0">
-<tr>
-<td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>
-<td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>
-<td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>
-<td bgcolor="#FFDD00"><a href="fimo.tsv""><b>Results in TSV Format</b></a></td>
-<td bgcolor="#FFDDFF"><a href="fimo.gff""><b>Results in GFF3 Format</b></a></td>
-</tr>
+    <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>
-<center><big><b>FIMO - Motif search tool</b></big></center>
-FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700)
-For further information on how to interpret these results please access <a href="http://meme-suite.org/doc/fimo-output-format.html">http://meme-suite.org/doc/fimo-output-format.html</a>.<br>
-To get a copy of the FIMO software please access <a href="http://meme-suite.org">http://meme-suite.org</a>
-<p>If you use FIMO in your research, please cite the following paper:<br>
-Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
-"FIMO: Scanning for occurrences of a given motif",
-<i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
-<center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
-  Database contains 1 sequences, 16569 residues
-  <table>
-    <thead>
-    </thead>
-    <tbody>
-    </tbody>
-  </table>
-A 0.278 C 0.222 G 0.222 T 0.278 </p>
-<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
-There were 11 motif occurences with a p-value less than 0.0001.
-The full set of motif occurences can be seen in the
-TSV (tab-delimited values) output file
-the GFF3 file 
-which may be suitable for uploading to the 
-(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
-or the XML file 
-The <i>p</i>-value of a motif occurrence is defined as the
-probability of a random sequence of the same length as the motif
-matching that position of the sequence with as good or better a score.
-The score for the match of a position in a sequence to a motif
-is computed by summing the appropriate entries from each column of
-the position-dependent scoring matrix that represents the motif.
-The q-value of a motif occurrence is defined as the
-false discovery rate if the occurrence is accepted as significant.
-<li>The table is sorted by increasing <i>p</i>-value.</li>
-<th>Motif ID</th>
-<th>Alt ID</th>
-<th>Sequence Name</th>
-<th>Strand</th>
-<th>Start</th>
-<th>End</th>
-<th>p-value</th>
-<th>q-value</th>
-<th>Matched Sequence</th>
-    <tr>
-      <td style="text-align:left;">CCAGCAY</td>
-      <td style="text-align:left;">DREME-5</td>
-      <td style="text-align:left;">chrM</td>
-      <td style="text-align:center;">+</td>
-      <td style="text-align:left;">510</td>
-      <td style="text-align:left;">516</td>
-      <td style="text-align:left;">4.15e-05</td>
-      <td style="text-align:left;">0.683</td>
-      <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAC</td>
-      <td style="text-align:left;">2093</td>
-      <td style="text-align:left;">2099</td>
-      <td style="text-align:left;">8.2e-05</td>
-      <td style="text-align:left;">0.332</td>
-      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
-   </tr>
-<hr>
-<center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
-Command line:
-Settings:
+</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>
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/fimo_output_test2.txt
--- a/test-data/fimo_output_test2.txt Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/fimo_output_test2.txt Sat Apr 09 08:32:23 2022 +0000
b
@@ -9,4 +9,4 @@
 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
+CCAGCAY DREME-5 chrM 4241 4247 + 13.1461 9.37e-05 1 CCAGCAT
\ No newline at end of file
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/fimo_output_test2.xml
--- a/test-data/fimo_output_test2.xml Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/fimo_output_test2.xml Sat Apr 09 08:32:23 2022 +0000
b
@@ -1,11 +1,3 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!-- Begin document body -->
-<fimo version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700">
-  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
->
-<settings>
-<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>
@@ -39,11 +31,4 @@
 <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"/>
-<value letter="A">0.278</value>
-<value letter="C">0.222</value>
-<value letter="G">0.222</value>
-<value letter="T">0.278</value>
-</background>
-<cisml-file>cisml.xml</cisml-file>
-</fimo>
+<motif name="GMATGT" alt="DREME-6" width="6" best-possible-match="GAATGT"/>
\ No newline at end of file
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/fimo_output_test3.html
--- a/test-data/fimo_output_test3.html Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/fimo_output_test3.html Sat Apr 09 08:32:23 2022 +0000
b
@@ -1,92 +1,23 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html xmlns:cis="http://zlab.bu.edu/schema/cisml" xmlns:fimo="http://noble.gs.washington.edu/schema/cisml" xmlns:mem="http://noble.gs.washington.edu/meme">
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="UTF-8">
-<title>FIMO Results</title>
-<style type="text/css">
-</head>
-<body color="#000000">
-<td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>
-<td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>
-<td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>
-<td bgcolor="#FFDD00"><a href="fimo.tsv""><b>Results in TSV Format</b></a></td>
-<td bgcolor="#FFDDFF"><a href="fimo.gff""><b>Results in GFF3 Format</b></a></td>
-<center><big><b>FIMO - Motif search tool</b></big></center>
-FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700)
-For further information on how to interpret these results please access <a href="http://meme-suite.org/doc/fimo-output-format.html">http://meme-suite.org/doc/fimo-output-format.html</a>.<br>
-To get a copy of the FIMO software please access <a href="http://meme-suite.org">http://meme-suite.org</a>
-<p>If you use FIMO in your research, please cite the following paper:<br>
-Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
-"FIMO: Scanning for occurrences of a given motif",
-<i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
-<center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
-  Database contains 1 sequences, 16569 residues
-  <table>
-    <thead>
-      <tr>
-        <th style="border-bottom: 1px dashed;">MOTIF</th>
-        <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>
-        <th style="border-bottom: 1px dashed; padding-left: 1em;text-align:left;" >
-         BEST POSSIBLE MATCH
-        </th>
-      </tr>
-    </thead>
-    <tbody>
-      <tr>
-        <td style="text-align:right;">ACTAAYH</td>
-        <td style="text-align:right;padding-left: 1em;">7</td>
-        <td style="text-align:left;padding-left: 1em;">ACTAACA</td>
-       </tr>
-    </tbody>
-  </table>
-</p>
-<p>
-Random model letter frequencies (--uniform--):
-A 0.250 C 0.250 G 0.250 T 0.250 </p>
-<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
-There were 517 motif occurences with a p-value less than 0.01.
-The full set of motif occurences can be seen in the
-TSV (tab-delimited values) output file
-the GFF3 file 
-which may be suitable for uploading to the 
-(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
-or the XML file 
-The <i>p</i>-value of a motif occurrence is defined as the
-probability of a random sequence of the same length as the motif
-matching that position of the sequence with as good or better a score.
-The score for the match of a position in a sequence to a motif
-is computed by summing the appropriate entries from each column of
-the position-dependent scoring matrix that represents the motif.
-The q-value of a motif occurrence is defined as the
-false discovery rate if the occurrence is accepted as significant.
-<li>The table is sorted by increasing <i>p</i>-value.</li>
-<table border="1">
-<thead>
-<tr>
-<th>Motif ID</th>
-<th>Alt ID</th>
-<th>Sequence Name</th>
-<th>Strand</th>
-<th>Start</th>
-<th>End</th>
-<th>p-value</th>
-<th>q-value</th>
-<th>Matched Sequence</th>
-</tr>
-</thead>
-<tbody>
-    <tr>
-      <td style="text-align:left;">ACTAAYH</td>
-      <td style="text-align:left;">DREME-1</td>
-      <td style="text-align:left;">chrM</td>
-      <td style="text-align:center;">+</td>
-      <td style="text-align:left;">440</td>
-      <td style="text-align:left;">446</td>
-      <td style="text-align:left;">6.1e-05</td>
-      <td style="text-align:left;">0.239</td>
-      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
-This information can be useful in the event you wish to report a
-problem with the FIMO software.
-</body>
-</html>
+    <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
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/fimo_output_test3.txt
--- a/test-data/fimo_output_test3.txt Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/fimo_output_test3.txt Sat Apr 09 08:32:23 2022 +0000
b
@@ -20,3 +20,21 @@
 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
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/fimo_output_test3.xml
--- a/test-data/fimo_output_test3.xml Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/fimo_output_test3.xml Sat Apr 09 08:32:23 2022 +0000
b
@@ -1,23 +1,3 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!-- Begin document body -->
-<fimo version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700">
-  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
->
-<settings>
-<setting name="background file name">--uniform--</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">0.01</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>
-<setting name="selected motif">ACTAAYH</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"/>
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/meme_output_test1.html
--- a/test-data/meme_output_test1.html Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/meme_output_test1.html Sat Apr 09 08:32:23 2022 +0000
[
@@ -1,24 +1,73 @@
-<!DOCTYPE HTML>
-<html>
-  <head>
-    <meta charset="UTF-8">
-    <title>MEME</title>
-    <script>
-      // @JSON_VAR data
-      var data = {
-        "program": "MEME",
-        "version": "5.0.5",
-        "release": "Mon Mar 18 20:12:19 2019 -0700",
-        "stop_reason": "Stopped because requested number of motifs (1) found.",
-        "cmd": [
-          "meme",
-          "-o",
-          "-nostatus", "-maxsize", "1000000"
-        ],
-        "options": {
-        },
-        "motifs": [
-        "scan": [
-    </script>
-var site_url = "http://meme-suite.org";
-
+      <script>
+      {
+        $("opt_mod").className = data.options.mod;
+        $("opt_objfun").textContent = data.options.objfun;
+        $("opt_spfun").textContent = data.options.spfun;
+        $("opt_strand").className = (current_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");
+        $("opt_nmotifs").textContent = data.options.nmotifs;
+        $("opt_evt").textContent = (typeof data.options.evt === "number" ? data.options.evt : "no limit");
+        $("opt_minw").textContent = data.options.minw;
+        $("opt_maxw").textContent = data.options.maxw;
+        $("opt_minsites").textContent = data.options.minsites;
+        $("opt_maxsites").textContent = data.options.maxsites;
+        $("opt_wnsites").textContent = data.options.wnsites;
+        $("opt_spmap").className = data.options.spmap;
+        $("opt_spfuzz").textContent = data.options.spfuzz;
+        $("opt_prior").className = data.options.prior;
+        if (data.options.prior == "dirichlet") {
+          $("opt_prior_source").textContent = make_background_source("Source", data.background.source, true);
+        } else {
+          $("opt_prior_source").textContent = (data.options.prior == "addone") ? "motif observed frequencies" : data.options.priors_source;
+        }
+        $("opt_b").textContent = (data.options.b < 0) ? "not applicable" : (data.options.b == 0) ? "intrinsic strength" : data.options.b;
+        $("opt_maxiter").textContent = data.options.maxiter;
+        $("opt_distance").textContent = data.options.distance;
+        $("opt_searchsize").textContent = data.options.searchsize;
+        if (typeof data.options.csites != "undefined") {
+          $("opt_csites").textContent = data.options.csites;
+        } else {
+          $("opt_csites").parentElement.style.display = "none"
+        }
+        if (typeof data.options.wg != "undefined") {
+          $("opt_wg").textContent = data.options.wg;
+        } else {
+          $("opt_wg").parentElement.style.display = "none"
+        }
+        if (typeof data.options.ws != "undefined") {
+          $("opt_ws").textContent = data.options.ws;
+        }
+        else {
+          $("opt_ws").parentElement.style.display = "none"
+        }
+        if (typeof data.options.noendgaps != "undefined") {
+          $("opt_noendgaps").className = (data.options.noendgaps ? "on" : "off");
+        }
+        else {
+          $("opt_noendgaps").parentElement.style.display = "none"
+        }
+        $("opt_substring").className = (data.options.substring ? "on" : "off");
+      }
+      </script>
+    </div>
+    <!-- list information on this program -->
+    <div id="info_sec" class="bar">
+      <div class="subsection">
+        <h5 id="version">MEME version</h5>
+        <span id="ins_version"></span> 
+        (Release date: <span id="ins_release"></span>)<br>
+      </div>
+      <script>
+        $("ins_version").innerHTML = data["version"];
+        $("ins_release").innerHTML = data["release"];
+      </script>
+      <div class="subsection" id="reference"> <script>print_citation("reference", "MEME");</script></div>
+      <div class="subsection">
+        <h5 id="command">Command line</h5>
+        <textarea id="cmd" rows="5" style="width:100%;" readonly="readonly">
+        </textarea>
+        <script>$("cmd").value = data["cmd"].join(" ");</script>
+      </div>
+    </div>
+    
+  </body>
+</html>
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/meme_output_test1.txt
--- a/test-data/meme_output_test1.txt Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/meme_output_test1.txt Sat Apr 09 08:32:23 2022 +0000
[
@@ -1,61 +1,39 @@
 ********************************************************************************
-MEME - Motif discovery tool
-MEME version 5.0.5 (Release date: Mon Mar 18 20:12:19 2019 -0700)
-REFERENCE
-TRAINING SET
-CONTROL SEQUENCES= --none--
-ALPHABET= ACDEFGHIKLMNPQRSTVWY
-Sequence name            Weight Length  Sequence name            Weight Length  
--------------            ------ ------  -------------            ------ ------  
-chr21_19617074_19617124_ 1.0000     50  chr21_26934381_26934431_ 1.0000     50  
-COMMAND LINE SUMMARY
-model:  mod=         zoops    nmotifs=         1    evt=           inf
-objective function:           em=       E-value of product of p-values
-                              starts=   E-value of product of p-values
-width:  minw=            8    maxw=           50
-nsites: minsites=        2    maxsites=       30    wnsites=       0.8
-theta:  spmap=         pam    spfuzz=        120
-em:     prior=       megap    b=            7500    maxiter=        50
-        distance=    1e-05
-trim:   wg=             11    ws=              1    endgaps=       yes
-data:   n=            1500    N=              30
-sample: seed=            0    hsfrac=          0
-        searchsize=   1500    norand=         no    csites=       1000
-Dirichlet mixture priors file: prior30.plib
-Letter frequencies in dataset:
-A 0.294 C 0.231 D 0 E 0 F 0 G 0.257 H 0 I 0 K 0 
-L 0 M 0 N 0 P 0 Q 0 R 0 S 0 T 0.217 V 0 
-W 0 Y 0 
-Background letter frequencies (from file dataset with add-one prior applied):
-A 0.291 C 0.229 D 0.000658 E 0.000658 F 0.000658 G 0.255 H 0.000658 I 0.000658 K 0.000658 
-L 0.000658 M 0.000658 N 0.000658 P 0.000658 Q 0.000658 R 0.000658 S 0.000658 T 0.215 V 0.000658 
-W 0.000658 Y 0.000658 
-Background model order: 0
-MOTIF GGGGTATAAAA MEME-1 width =  11  sites =  25  llr = 239  E-value = 2.4e-011
+SUMMARY OF MOTIFS
+********************************************************************************
+
 --------------------------------------------------------------------------------
- Motif GGGGTATAAAA MEME-1 Description
- Motif GGGGTATAAAA MEME-1 sites sorted by position p-value
-Sequence name             Start   P-value               Site  
--------------             ----- ---------            -----------
-chr21_46046964_46047014_     13  1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
- Motif GGGGTATAAAA MEME-1 block diagrams
-SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
--------------            ----------------  -------------
-chr21_46046964_46047014_          1.1e-06  12_[1]_27
- Motif GGGGTATAAAA MEME-1 in BLOCKS format
-BL   MOTIF GGGGTATAAAA width=11 seqs=25
-chr21_46046964_46047014_ (   13) GGGGTATAAAA  1 
- Motif GGGGTATAAAA MEME-1 position-specific scoring matrix
-log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011 
-   -32   -680     91     77      7    138    -20     55     64    107     11    150    142     72     87    396   -148    221   -140    -36 
- Motif GGGGTATAAAA MEME-1 position-specific probability matrix
-letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011 
- 0.240000  0.000000  0.000000  0.000000  0.000000  0.680000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.080000  0.000000  0.000000  0.000000 
- Motif GGGGTATAAAA MEME-1 regular expression
-[GA][GA][GC][GA]TATA[AT]AA
-SUMMARY OF MOTIFS
  Combined block diagrams: non-overlapping sites with p-value < 0.0001
+--------------------------------------------------------------------------------
 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 -------------            ----------------  -------------
 chr21_19617074_19617124_         1.22e-03  39_[1(3.06e-05)]
-Stopped because requested number of motifs (1) found.
+chr21_26934381_26934431_         2.21e-03  27_[1(5.52e-05)]_12
+chr21_28217753_28217803_         7.29e-01  50
+chr21_31710037_31710087_         2.37e-03  14_[1(5.94e-05)]_25
+chr21_31744582_31744632_         1.22e-03  12_[1(3.06e-05)]_27
+chr21_31768316_31768366_         1.53e-03  [1(3.82e-05)]_39
+chr21_31914206_31914256_         6.70e-04  15_[1(1.68e-05)]_24
+chr21_31933633_31933683_         1.81e-03  4_[1(4.54e-05)]_35
+chr21_31962741_31962791_         1.61e-02  50
+chr21_31964683_31964733_         1.36e-04  13_[1(3.41e-06)]_26
+chr21_31973364_31973414_         1.99e-01  50
+chr21_31992870_31992920_         3.47e-04  16_[1(8.67e-06)]_23
+chr21_32185595_32185645_         3.47e-04  18_[1(8.67e-06)]_21
+chr21_32202076_32202126_         2.01e-04  13_[1(5.01e-06)]_26
+chr21_32253899_32253949_         8.11e-04  19_[1(2.03e-05)]_20
+chr21_32410820_32410870_         3.47e-04  21_[1(8.67e-06)]_18
+chr21_36411748_36411798_         2.71e-03  22_[1(6.78e-05)]_17
+chr21_37838750_37838800_         8.23e-02  50
+chr21_45705687_45705737_         1.53e-03  37_[1(3.82e-05)]_2
+chr21_45971413_45971463_         1.36e-04  9_[1(3.41e-06)]_30
+chr21_45978668_45978718_         6.37e-04  4_[1(1.59e-05)]_35
+chr21_45993530_45993580_         1.60e-04  7_[1(4.00e-06)]_32
+chr21_46020421_46020471_         4.83e-04  2_[1(1.21e-05)]_37
+chr21_46031920_46031970_         2.43e-04  15_[1(6.06e-06)]_24
+chr21_46046964_46047014_         4.26e-05  12_[1(1.06e-06)]_27
+chr21_46057197_46057247_         1.36e-04  36_[1(3.41e-06)]_3
+chr21_46086869_46086919_         4.30e-02  50
+chr21_46102103_46102153_         4.30e-02  50
+chr21_47517957_47518007_         6.37e-04  32_[1(1.59e-05)]_7
+chr21_47575506_47575556_         1.61e-03  30_[1(4.02e-05)]_9
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/meme_output_test1.xml
--- a/test-data/meme_output_test1.xml Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/meme_output_test1.xml Sat Apr 09 08:32:23 2022 +0000
[
b'@@ -1,118 +1,58 @@\n-<?xml version=\'1.0\' encoding=\'UTF-8\' standalone=\'yes\'?>\n-<!-- Document definition -->\n-<!DOCTYPE MEME[\n-<!ELEMENT MEME (\n-  training_set,\n-  model, \n-  motifs, \n-  scanned_sites_summary?\n-)>\n-<!ATTLIST MEME \n-  version CDATA #REQUIRED\n-  release CDATA #REQUIRED\n-<!-- Training-set elements -->\n-<!ELEMENT training_set (alphabet, ambigs, sequence*, letter_frequencies)>\n-                   name CDATA #REQUIRED\n-                   length CDATA #REQUIRED\n-                   weight CDATA #REQUIRED\n-<!ELEMENT letter_frequencies (alphabet_array)>\n-<!-- Model elements -->\n-<!ELEMENT model (\n-  command_line,\n-  host,\n-  type,\n-  nmotifs,\n-)>\n-<!ELEMENT command_line (#PCDATA)*>\n-<!ELEMENT host (#PCDATA)*>\n-<!ELEMENT type (#PCDATA)*>\n-<!ELEMENT nmotifs (#PCDATA)*>\n-<!-- The left_flank contains the sequence for 10 bases to the left of the motif start -->\n-<!ELEMENT left_flank (#PCDATA)>\n-<!-- The site contains the sequence for the motif instance -->\n-<!ELEMENT site (letter_ref*)>\n-<!-- The right_flank contains the sequence for 10 bases to the right of the motif end -->\n-<!ELEMENT right_flank (#PCDATA)>\n-<!-- Scanned site elements -->\n-<!-- Scanned sites are motif occurences found during the sequence scan phase -->\n-<!ELEMENT scanned_sites_summary (scanned_sites*)>\n-<!ATTLIST scanned_sites_summary p_thresh CDATA #REQUIRED>\n-<!ELEMENT scanned_sites (scanned_site*)>\n-<!ATTLIST scanned_sites sequence_id IDREF #REQUIRED\n-                        pvalue CDATA #REQUIRED\n-                        num_sites CDATA #REQUIRED>\n-<!ELEMENT scanned_site EMPTY>\n-<!ATTLIST scanned_site  motif_id IDREF #REQUIRED\n-                        strand (plus|minus|none) \'none\'\n-                        position CDATA #REQUIRED\n-                        pvalue CDATA #REQUIRED>\n-<!-- Utility elements -->\n-<!-- A reference to a letter in the alphabet -->\n-<!ELEMENT letter_ref EMPTY>\n-<!ATTLIST letter_ref letter_id IDREF #REQUIRED>\n-<!-- A alphabet-array contains one floating point value for each letter in an alphabet -->\n-<!ELEMENT alphabet_array (value*)>\n-<!ELEMENT value (#PCDATA)>\n-<!ATTLIST value letter_id IDREF #REQUIRED>\n-<!-- A alphabet_matrix contains one alphabet_array for each position in a motif -->\n-<!ELEMENT alphabet_matrix (alphabet_array*)>\n-]>\n-<!-- Begin document body -->\n-<MEME version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700">\n-<alphabet name="Protein" like="protein">\n-<letter id="A" symbol="A" name="Alanine" colour="0000CC"/>\n-</alphabet>\n-<sequence id="sequence_0" name="chr21_19617074_19617124_+" length="50" weight="1.000000" />\n-<letter_frequencies>\n-<alphabet_array>\n-<value letter_id="A">0.294</value>\n-</letter_frequencies>\n-</training_set>\n-<model>\n-<scores>\n-<alphabet_matrix>\n-<value letter_id="A">-32</value>\n-<value letter_id="A">-79</value>\n-<value letter_id="A">11</value>\n-<value letter_id="A">-596</value>\n-<value letter_id="A">165</value>\n-<value letter_id="A">-838</value>\n-<value letter_id="A">176</value>\n-<value letter_id="A">134</value>\n-<value letter_id="A">165</value>\n-<value letter_id="A">147</value>\n-<value letter_id="A">0.240000</value>\n-<value letter_id="A">0.280000</value>\n-<value letter_id="A">0.160000</value>\n-<value letter_id="A">0.320000</value>\n-<value letter_id="A">0.000000</value>\n-<value letter_id="A">0.960000</value>\n-<value letter_id="A">0.000000</value>\n-<value letter_id="A">1.000000</value>\n-<value letter_id="A">0.760000</value>\n-<value letter_id="A">0.960000</value>\n-<value letter_id="A">0.840000</value>\n-</alphabet_matrix>\n-</probabilities>\n-<regular_expression>\n-[GA][GA][GC][GA]TATA[AT]AA\n-</regular_expression>\n-<contributing_sites>\n-<contributing_site sequence_id="sequence_24" position="12" strand="none" pvalue="1.06e-06" >\n-<left_flank>AAGGCCAGGA</left_flank>\n-<site>\n-<letter_ref letter_id="G"/>\n-</site>\n-<right_flank>GCCTGAGAGC</right_flank>\n-</contributing_site>\n-<contributing_site sequence_id="sequence_25" position="36" strand="none" pvalue="3.41e-06" >\n-<left_flank>ACAGGCCCTG</left_flank'..b'="none" position="12" pvalue="3.06e-05"/>\n+</scanned_sites>\n <scanned_sites sequence_id="sequence_5" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="0" pvalue="3.82e-05"/>\n+</scanned_sites>\n <scanned_sites sequence_id="sequence_6" pvalue="6.70e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="1.68e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_7" pvalue="1.81e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="4" pvalue="4.54e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_8" pvalue="1.61e-02" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_9" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="13" pvalue="3.41e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_10" pvalue="1.99e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_11" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="16" pvalue="8.67e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_12" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="18" pvalue="8.67e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_13" pvalue="2.01e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="13" pvalue="5.01e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_14" pvalue="8.11e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="19" pvalue="2.03e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_15" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="21" pvalue="8.67e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_16" pvalue="2.71e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="22" pvalue="6.78e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_17" pvalue="8.23e-02" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_18" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="37" pvalue="3.82e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_19" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="9" pvalue="3.41e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_20" pvalue="6.37e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="4" pvalue="1.59e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_21" pvalue="1.60e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="7" pvalue="4.00e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_22" pvalue="4.83e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="2" pvalue="1.21e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_23" pvalue="2.43e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="6.06e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_24" pvalue="4.26e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="12" pvalue="1.06e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_25" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="36" pvalue="3.41e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_26" pvalue="4.30e-02" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_27" pvalue="4.30e-02" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_28" pvalue="6.37e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="32" pvalue="1.59e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_29" pvalue="1.61e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="30" pvalue="4.02e-05"/>\n+</scanned_sites>\n+</scanned_sites_summary>\n </MEME>\n'
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/meme_output_test2.html
--- a/test-data/meme_output_test2.html Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/meme_output_test2.html Sat Apr 09 08:32:23 2022 +0000
[
@@ -1,27 +1,73 @@
-<!DOCTYPE HTML>
-<html>
-  <head>
-    <meta charset="UTF-8">
-    <title>MEME</title>
-    <script>
-      // @JSON_VAR data
-      var data = {
-        "program": "MEME",
-        "version": "5.0.5",
-        "release": "Mon Mar 18 20:12:19 2019 -0700",
-        "stop_reason": "Stopped because requested number of motifs (1) found.",
-        "cmd": [
-          "meme",
-          "-o",
-          "-nostatus", "-maxsize", "1000000", "-sf", "Galaxy_FASTA_Input",
-          "-dna", "-mod", "zoops", "-nmotifs", "1", "-wnsites", "0.8",
-          "-minw", "8", "-maxw", "50", "-wg", "11", "-ws", "1", "-maxiter",
-          "50", "-distance", "0.001", "-prior", "dirichlet", "-b", "0.01",
-          "-plib",
-          "-spmap", "uni", "-spfuzz", "0.5"
-        ],
-        "motifs": [
-        ]
-      };
-    </script>
-var site_url = "http://meme-suite.org";
+      <script>
+      {
+        $("opt_mod").className = data.options.mod;
+        $("opt_objfun").textContent = data.options.objfun;
+        $("opt_spfun").textContent = data.options.spfun;
+        $("opt_strand").className = (current_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");
+        $("opt_nmotifs").textContent = data.options.nmotifs;
+        $("opt_evt").textContent = (typeof data.options.evt === "number" ? data.options.evt : "no limit");
+        $("opt_minw").textContent = data.options.minw;
+        $("opt_maxw").textContent = data.options.maxw;
+        $("opt_minsites").textContent = data.options.minsites;
+        $("opt_maxsites").textContent = data.options.maxsites;
+        $("opt_wnsites").textContent = data.options.wnsites;
+        $("opt_spmap").className = data.options.spmap;
+        $("opt_spfuzz").textContent = data.options.spfuzz;
+        $("opt_prior").className = data.options.prior;
+        if (data.options.prior == "dirichlet") {
+          $("opt_prior_source").textContent = make_background_source("Source", data.background.source, true);
+        } else {
+          $("opt_prior_source").textContent = (data.options.prior == "addone") ? "motif observed frequencies" : data.options.priors_source;
+        }
+        $("opt_b").textContent = (data.options.b < 0) ? "not applicable" : (data.options.b == 0) ? "intrinsic strength" : data.options.b;
+        $("opt_maxiter").textContent = data.options.maxiter;
+        $("opt_distance").textContent = data.options.distance;
+        $("opt_searchsize").textContent = data.options.searchsize;
+        if (typeof data.options.csites != "undefined") {
+          $("opt_csites").textContent = data.options.csites;
+        } else {
+          $("opt_csites").parentElement.style.display = "none"
+        }
+        if (typeof data.options.wg != "undefined") {
+          $("opt_wg").textContent = data.options.wg;
+        } else {
+          $("opt_wg").parentElement.style.display = "none"
+        }
+        if (typeof data.options.ws != "undefined") {
+          $("opt_ws").textContent = data.options.ws;
+        }
+        else {
+          $("opt_ws").parentElement.style.display = "none"
+        }
+        if (typeof data.options.noendgaps != "undefined") {
+          $("opt_noendgaps").className = (data.options.noendgaps ? "on" : "off");
+        }
+        else {
+          $("opt_noendgaps").parentElement.style.display = "none"
+        }
+        $("opt_substring").className = (data.options.substring ? "on" : "off");
+      }
+      </script>
+    </div>
+    <!-- list information on this program -->
+    <div id="info_sec" class="bar">
+      <div class="subsection">
+        <h5 id="version">MEME version</h5>
+        <span id="ins_version"></span> 
+        (Release date: <span id="ins_release"></span>)<br>
+      </div>
+      <script>
+        $("ins_version").innerHTML = data["version"];
+        $("ins_release").innerHTML = data["release"];
+      </script>
+      <div class="subsection" id="reference"> <script>print_citation("reference", "MEME");</script></div>
+      <div class="subsection">
+        <h5 id="command">Command line</h5>
+        <textarea id="cmd" rows="5" style="width:100%;" readonly="readonly">
+        </textarea>
+        <script>$("cmd").value = data["cmd"].join(" ");</script>
+      </div>
+    </div>
+    
+  </body>
+</html>
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/meme_output_test2.txt
--- a/test-data/meme_output_test2.txt Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/meme_output_test2.txt Sat Apr 09 08:32:23 2022 +0000
[
@@ -1,86 +1,40 @@
 ********************************************************************************
-MEME - Motif discovery tool
-MEME version 5.0.5 (Release date: Mon Mar 18 20:12:19 2019 -0700)
-REFERENCE
-TRAINING SET
-PRIMARY SEQUENCES= Galaxy_FASTA_Input
-CONTROL SEQUENCES= --none--
-ALPHABET= ACGT
-Sequence name            Weight Length  Sequence name            Weight Length  
--------------            ------ ------  -------------            ------ ------  
-chr21_19617074_19617124_ 1.0000     50  chr21_26934381_26934431_ 1.0000     50  
-COMMAND LINE SUMMARY
-model:  mod=         zoops    nmotifs=         1    evt=           inf
-objective function:           em=       E-value of product of p-values
-                              starts=   E-value of product of p-values
-strands: +
-width:  minw=            8    maxw=           50
-nsites: minsites=        2    maxsites=       30    wnsites=       0.8
-theta:  spmap=         uni    spfuzz=        0.5
-em:     prior=   dirichlet    b=            0.01    maxiter=        50
-        distance=    0.001
-trim:   wg=             11    ws=              1    endgaps=       yes
-data:   n=            1500    N=              30
-sample: seed=            0    hsfrac=          0
-        searchsize=   1500    norand=         no    csites=       1000
-Dirichlet mixture priors file:
-Letter frequencies in dataset:
-A 0.294 C 0.231 G 0.257 T 0.217 
-Background letter frequencies (from file dataset with add-one prior applied):
-A 0.294 C 0.231 G 0.257 T 0.217 
-Background model order: 0
-MOTIF GGSRTATAAAA MEME-1 width =  11  sites =  30  llr = 254  E-value = 5.1e-040
- Motif GGSRTATAAAA MEME-1 Description
-Simplified        A  3313:9:a798
-pos.-specific     C  1:3::1:::1:
-probability       G  6756::::::2
-matrix            T  1:11a1a:3::
+SUMMARY OF MOTIFS
+********************************************************************************
 
-         bits    2.2       *    
-                 2.0     * *    
-                 1.8     * *    
-                 1.5     * ** * 
-Relative         1.3     * ** * 
-Entropy          1.1     ****** 
-(12.2 bits)      0.9  *  *******
-                 0.7  *  *******
-                 0.4 ** ********
-                 0.2 ***********
-                 0.0 -----------
-
-Multilevel           GGGGTATAAAA
-consensus            AACA    T  
-sequence                        
- Motif GGSRTATAAAA MEME-1 sites sorted by position p-value
-Sequence name             Start   P-value               Site  
-chr21_46046964_46047014_     13  4.51e-07 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
- Motif GGSRTATAAAA MEME-1 block diagrams
-SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
+--------------------------------------------------------------------------------
+ Combined block diagrams: non-overlapping sites with p-value < 0.0001
+--------------------------------------------------------------------------------
+SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 -------------            ----------------  -------------
-chr21_46046964_46047014_          4.5e-07  12_[+1]_27
- Motif GGSRTATAAAA MEME-1 in BLOCKS format
-BL   MOTIF GGSRTATAAAA width=11 seqs=30
-chr21_46046964_46047014_ (   13) GGGGTATAAAA  1 
- Motif GGSRTATAAAA MEME-1 position-specific scoring matrix
-log-odds matrix: alength= 4 w= 11 n= 1200 bayes= 5.2854 E= 5.1e-040 
-   -14   -179    114   -112 
-     3  -1155    137   -270 
-  -114     20     86    -71 
-     3   -279    122   -170 
- -1155  -1155   -295    215 
-   156   -179  -1155   -170 
- -1155  -1155  -1155    220 
-   172   -279  -1155  -1155 
-   125  -1155  -1155     46 
-   167   -179  -1155  -1155 
-   144  -1155    -63   -270 
- Motif GGSRTATAAAA MEME-1 position-specific probability matrix
-letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 5.1e-040 
- 0.266667  0.066667  0.566667  0.100000 
- Motif GGSRTATAAAA MEME-1 regular expression
-[GA][GA][GC][GA]TATA[AT]AA
-SUMMARY OF MOTIFS
- Combined block diagrams: non-overlapping sites with p-value < 0.0001
-SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 chr21_19617074_19617124_         5.63e-04  39_[+1(1.41e-05)]
-Stopped because requested number of motifs (1) found.
+chr21_26934381_26934431_         1.57e-03  27_[+1(3.93e-05)]_12
+chr21_28217753_28217803_         1.00e-01  50
+chr21_31710037_31710087_         2.49e-03  14_[+1(6.24e-05)]_25
+chr21_31744582_31744632_         1.22e-03  12_[+1(3.04e-05)]_27
+chr21_31768316_31768366_         1.47e-03  [+1(3.67e-05)]_39
+chr21_31914206_31914256_         6.45e-04  15_[+1(1.61e-05)]_24
+chr21_31933633_31933683_         2.26e-03  4_[+1(5.65e-05)]_35
+chr21_31962741_31962791_         3.37e-02  50
+chr21_31964683_31964733_         1.95e-04  13_[+1(4.86e-06)]_26
+chr21_31973364_31973414_         5.73e-02  50
+chr21_31992870_31992920_         5.52e-04  16_[+1(1.38e-05)]_23
+chr21_32185595_32185645_         2.59e-04  18_[+1(6.48e-06)]_21
+chr21_32202076_32202126_         1.10e-04  13_[+1(2.74e-06)]_26
+chr21_32253899_32253949_         7.78e-04  17_[+1(1.95e-05)]_22
+chr21_32410820_32410870_         5.52e-04  21_[+1(1.38e-05)]_18
+chr21_36411748_36411798_         2.85e-03  22_[+1(7.15e-05)]_17
+chr21_37838750_37838800_         1.90e-02  50
+chr21_45705687_45705737_         8.63e-04  37_[+1(2.16e-05)]_2
+chr21_45971413_45971463_         1.95e-04  9_[+1(4.86e-06)]_30
+chr21_45978668_45978718_         2.59e-04  4_[+1(6.48e-06)]_35
+chr21_45993530_45993580_         1.95e-04  7_[+1(4.86e-06)]_32
+chr21_46020421_46020471_         7.78e-04  2_[+1(1.95e-05)]_37
+chr21_46031920_46031970_         8.89e-05  15_[+1(2.22e-06)]_24
+chr21_46046964_46047014_         1.80e-05  12_[+1(4.51e-07)]_27
+chr21_46057197_46057247_         1.95e-04  36_[+1(4.86e-06)]_3
+chr21_46086869_46086919_         5.54e-03  50
+chr21_46102103_46102153_         5.54e-03  50
+chr21_47517957_47518007_         2.59e-04  32_[+1(6.48e-06)]_7
+chr21_47575506_47575556_         1.22e-03  30_[+1(3.04e-05)]_9
+--------------------------------------------------------------------------------
\ No newline at end of file
b
diff -r d7a6ea1e3b9d -r c5209f38700d test-data/meme_output_test2.xml
--- a/test-data/meme_output_test2.xml Sat Nov 27 14:37:42 2021 +0000
+++ b/test-data/meme_output_test2.xml Sat Apr 09 08:32:23 2022 +0000
[
b'@@ -1,82 +1,58 @@\n-<?xml version=\'1.0\' encoding=\'UTF-8\' standalone=\'yes\'?>\n-<!-- Document definition -->\n-<!DOCTYPE MEME[\n-<!ELEMENT MEME (\n-  training_set,\n-  model, \n-  motifs, \n-  scanned_sites_summary?\n-)>\n-<!ATTLIST MEME \n-  version CDATA #REQUIRED\n-  release CDATA #REQUIRED\n-<!-- Training-set elements -->\n-<!ELEMENT training_set (alphabet, ambigs, sequence*, letter_frequencies)>\n-<!ATTLIST training_set primary_sequences CDATA #REQUIRED primary_count CDATA #REQUIRED primary_positions CDATA #REQUIRED\n-  control_sequences CDATA "" control_count CDATA "" control_positions CDATA "">\n-<!ELEMENT alphabet (letter*)>\n-<!ATTLIST alphabet name CDATA #REQUIRED>\n-<!ELEMENT letter_frequencies (alphabet_array)>\n-<!-- Model elements -->\n-<!ELEMENT model (\n-  command_line,\n-  host,\n-  type,\n-  nmotifs,\n-)>\n-<!ELEMENT command_line (#PCDATA)*>\n-<!ELEMENT motifs (motif*)>\n-<!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)>\n-<!-- The left_flank contains the sequence for 10 bases to the left of the motif start -->\n-<!ELEMENT left_flank (#PCDATA)>\n-<!-- The site contains the sequence for the motif instance -->\n-<!ELEMENT site (letter_ref*)>\n-<!-- The right_flank contains the sequence for 10 bases to the right of the motif end -->\n-<!ELEMENT right_flank (#PCDATA)>\n-<!-- Scanned site elements -->\n-<!-- Scanned sites are motif occurences found during the sequence scan phase -->\n-<!ELEMENT scanned_sites_summary (scanned_sites*)>\n-<training_set primary_sequences="Galaxy_FASTA_Input" primary_count="30" primary_positions="1500" control_sequences="--none--" control_count="0" control_positions="0">\n-<alphabet name="DNA" like="dna">\n-<letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>\n-<sequence id="sequence_0" name="chr21_19617074_19617124_+" length="50" weight="1.000000" />\n-<value letter_id="G">0.257</value>\n-<value letter_id="T">0.217</value>\n-</alphabet_array>\n-<model>\n-<type>zoops</type>\n-<scores>\n-<alphabet_matrix>\n-<alphabet_array>\n-<value letter_id="A">-14</value>\n-<value letter_id="A">3</value>\n-<value letter_id="A">-1155</value>\n-<value letter_id="A">156</value>\n-<value letter_id="A">-1155</value>\n-<value letter_id="A">172</value>\n-<value letter_id="A">125</value>\n-<value letter_id="A">167</value>\n-<value letter_id="A">144</value>\n-<value letter_id="A">0.266667</value>\n-<value letter_id="A">0.300000</value>\n-<value letter_id="A">0.800000</value>\n-<contributing_site sequence_id="sequence_24" position="12" strand="plus" pvalue="4.51e-07" >\n-<left_flank>AAGGCCAGGA</left_flank>\n-<letter_ref letter_id="G"/>\n-<right_flank>GCCTGAGAGC</right_flank>\n-<contributing_site sequence_id="sequence_23" position="15" strand="plus" pvalue="2.22e-06" >\n-<letter_ref letter_id="A"/>\n-<contributing_site sequence_id="sequence_13" position="13" strand="plus" pvalue="2.74e-06" >\n-<right_flank>AGCCCTGTAC</right_flank>\n-<contributing_site sequence_id="sequence_25" position="36" strand="plus" pvalue="4.86e-06" >\n-<left_flank>CGTGGTCGCG</left_flank>\n-<right_flank>GC</right_flank>\n-<contributing_site sequence_id="sequence_29" position="30" strand="plus" pvalue="3.04e-05" >\n-<left_flank>GCTGCCGGTG</left_flank>\n-<right_flank>GCCCTGGCG</right_flank>\n-<contributing_site sequence_id="sequence_4" position="12" strand="plus" pvalue="3.04e-05" >\n+</motifs>\n <scanned_sites_summary p_thresh="0.0001">\n <scanned_sites sequence_id="sequence_0" pvalue="5.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="39" pvalue="1.41e-05"/>\n+</scanned_sites>\n <scanned_sites sequence_id="sequence_1" pvalue="1.57e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="27" pvalue="3.93e-05"/>\n+</scanned_sites>\n <scanned_sites sequence_id="sequence_2" pvalue="1.00e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_3" pvalue="2.49e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="14" pvalue="6.24e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequen'..b'="plus" position="12" pvalue="3.04e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_5" pvalue="1.47e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="0" pvalue="3.67e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_6" pvalue="6.45e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="1.61e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_7" pvalue="2.26e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="5.65e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_8" pvalue="3.37e-02" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_9" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="4.86e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_10" pvalue="5.73e-02" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_11" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="16" pvalue="1.38e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_12" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="18" pvalue="6.48e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_13" pvalue="1.10e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="2.74e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_14" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="17" pvalue="1.95e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_15" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="21" pvalue="1.38e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_16" pvalue="2.85e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="22" pvalue="7.15e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_17" pvalue="1.90e-02" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_18" pvalue="8.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="37" pvalue="2.16e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_19" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="9" pvalue="4.86e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_20" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="6.48e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_21" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="7" pvalue="4.86e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_22" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="2" pvalue="1.95e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_23" pvalue="8.89e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="2.22e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_24" pvalue="1.80e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="4.51e-07"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_25" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="36" pvalue="4.86e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_26" pvalue="5.54e-03" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_27" pvalue="5.54e-03" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_28" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="32" pvalue="6.48e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_29" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="30" pvalue="3.04e-05"/>\n+</scanned_sites>\n+</scanned_sites_summary>\n </MEME>\n'