diff test-data/dreme_output_test2.html @ 18:19237efe98d1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
author iuc
date Sat, 09 Apr 2022 08:34:02 +0000
parents 3f0dd362b755
children
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--- a/test-data/dreme_output_test2.html	Sat Nov 27 14:38:35 2021 +0000
+++ b/test-data/dreme_output_test2.html	Sat Apr 09 08:34:02 2022 +0000
@@ -1,167 +1,50 @@
-<!DOCTYPE HTML>
-<html>
-  <head>
-    <meta charset="UTF-8">
-    <title>DREME</title>
-    <script>
-      // @JSON_VAR data
-      var data = {
-        "program": "dreme",
-        "version": "5.0.5",
-        "release": "Mon Mar 18 20:12:19 2019 -0700",
-        "cmd": [
-          "dreme", "-o", "./dreme_out", "-p",
-          "-norc", "-rna", "-s", "1", "-e", "1e-05", "-g", "100", "-mink",
-          "4", "-maxk", "10"
-        ],
-        "options": {
-          "revcomp": false,
-          "ngen": 100,
-          "add_pv_thresh": 0.01,
-          "seed": 1,
-          "stop": {
-            "evalue": "1e-05"
-          }
-        },
-        "alphabet": {
-          "name": "RNA",
-          "like": "rna",
-          "ncore": 4,
-          "symbols": [
-            {
-              "symbol": "A",
-              "name": "Adenine",
-              "colour": "CC0000"
-            }, {
-              "symbol": "C",
-              "name": "Cytosine",
-              "colour": "0000CC"
-              "symbol": "G",
-              "name": "Guanine",
-              "colour": "FFB300"
-              "symbol": "U",
-              "aliases": "T",
-              "name": "Uracil",
-              "colour": "008000"
-              "symbol": "N",
-              "aliases": "X.",
-              "name": "Any base",
-              "equals": "ACGU"
-              "symbol": "V",
-              "name": "Not U",
-              "equals": "ACG"
-              "symbol": "H",
-              "name": "Not G",
-              "equals": "ACU"
-              "symbol": "D",
-              "name": "Not C",
-              "equals": "AGU"
-              "symbol": "B",
-              "name": "Not A",
-              "equals": "CGU"
-              "symbol": "M",
-              "name": "Amino",
-              "equals": "AC"
-              "symbol": "R",
-              "name": "Purine",
-              "equals": "AG"
-              "symbol": "W",
-              "name": "Weak",
-              "equals": "AU"
-              "symbol": "S",
-              "name": "Strong",
-              "equals": "CG"
-              "symbol": "Y",
-              "name": "Pyrimidine",
-              "equals": "CU"
-              "symbol": "K",
-              "name": "Keto",
-              "equals": "GU"
-        "background": {
-          "freqs": [0.221, 0.245, 0.221, 0.312]
-        "sequence_db": {
-          "count": 1000
-        "control_db": {
-          "name": "shuffled positive sequences",
-          "from": "shuffled",
-          "count": 1000,
-          "freqs": [0.221, 0.245, 0.221, 0.312]
-        "motifs": [
-            "db": 0,
-            "id": "UUYUCY",
-            "alt": "DREME-1",
-            "len": 6,
-            "nsites": 459,
-            "evalue": "3.3e-013",
-            "p": 387,
-            "n": 210,
-            "pvalue": "2.6e-018",
-            "unerased_evalue": "3.3e-013",
-            "pwm": [
-              [0.000000, 0.000000, 0.000000, 1.000000], 
-              [0.000000, 0.000000, 0.000000, 1.000000], 
-              [0.000000, 0.294118, 0.000000, 0.705882], 
-              [0.000000, 0.000000, 0.000000, 1.000000], 
-              [0.000000, 1.000000, 0.000000, 0.000000], 
-              [0.000000, 0.474946, 0.000000, 0.525054]
-            "matches": [
-                "seq": "UUUUCC",
-                "p": 147,
-                "n": 75,
-                "pvalue": "1.8e-007",
-                "evalue": "2.2e-002"
-    </script>
-var site_url = "http://meme-suite.org";
-//======================================================================
-// end RasterizedAlphabet
-//======================================================================
-//======================================================================
-// start LogoMetrics object
-//======================================================================
- * Initialise and display the download popup.
-</style>
-  </head>
-  <body data-scrollpad="true">
-    <!--  -->
-    <div id="grey_out_page" class="grey_background" style="display:none;">
-        The name of the motif uses the IUPAC codes for nucleotides which has 
-        a different letter to represent each of the 15 possible combinations.
-        The name is itself a representation of the motif though the position
-        weight matrix is not directly equivalent as it is generated from the
-        sites found that matched the letters given in the name.
-      <p>The logo of the motif.</p>
-      <p>The logo of the reverse complement motif.</p>
-      <p>The E-value is the enrichment p-value times the number of candidate 
-        motifs tested.</p>
-      <p>The enrichment p-value is calculated using Fisher's Exact Test for 
-        enrichment of the motif in the positive sequences.</p>
-      <p>Note that the counts used in Fisher's Exact Test are made after 
-        erasing sites that match previously found motifs.</p>
-      <p>The E-value of the motif calculated without erasing the sites of 
-        previously found motifs.</p>
-      <p>Show more information on the motif.</p>
-      <p>Submit your motif to another MEME Suite program or download your motif.</p>
-      <h5>Supported Programs</h5>
-        <dt>Tomtom</dt>
-        <dd>Tomtom is a tool for searching for similar known motifs. 
-        <dt>MAST</dt>
-        <dd>MAST is a tool for searching biological sequence databases for 
-          sequences that contain one or more of a group of known motifs.
-        <dt>FIMO</dt>
-        <dd>FIMO is a tool for searching biological sequence databases for 
-          sequences that contain one or more known motifs.
-        <dt>GOMo</dt>
-        <dd>GOMo is a tool for identifying possible roles (Gene Ontology 
-          terms) for DNA binding motifs.
-        <dt>SpaMo</dt>
-        <dd>SpaMo is a tool for inferring possible transcription factor
-          complexes by finding motifs with enriched spacings.
-    <!-- Page starts here -->
-        <h1>DREME</h1>
-        <h2>Discriminative Regular Expression Motif Elicitation</h2>
-        For further information on how to interpret these results please access
-        To get a copy of the MEME software please access 
-        If you use DREME in your research please cite the following paper:<br />
-          Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011.
+      <h4>Other Settings</h4>
+      <table id="tbl_settings" class="inputs hide_advanced">
+        <tr>
+          <th>Strand Handling</th>
+          <td id="opt_strand">
+            <span class="strand_none">This alphabet only has one strand</span>
+            <span class="strand_given">Only the given strand is processed</span>
+            <span class="strand_both">Both the given and reverse complement strands are processed</span>
+          </td>
+        </tr>
+        <tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr>
+        <tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr>
+        <tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr>
+        <tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr>
+        <tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr>
+      </table>
+      <script>
+      {
+        $("opt_strand").className = (current_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");
+        $("opt_ngen").innerHTML = data.options.ngen;
+        $("opt_seed").innerHTML = data.options.seed;
+        $("opt_stop_evalue").innerHTML = data.options.stop.evalue;
+        $("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count.");
+        $("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time.");
+      }
+      </script>
+    </div>
+    <!-- list information on this program -->
+    <div id="info_sec" class="bar" style="position:relative">
+      <div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div>
+      <div class="subsection">
+        <h5 id="version">DREME version</h5>
+        <span id="ins_version"></span> 
+        (Release date: <span id="ins_release"></span>)<br>
+      </div>
+      <script>
+        $("ins_version").innerHTML = data["version"];
+        $("ins_release").innerHTML = data["release"];
+      </script>
+      <div class="subsection" id="reference"> <script>print_citation("reference", "DREME");</script> </div>
+      <div class="subsection">
+        <h5 id="command">Command line</h5>
+        <textarea id="cmd" rows="3" style="width:100%;" readonly="readonly">
+        </textarea>
+        <script>$("cmd").value = data["cmd"].join(" ");</script>
+      </div>
+    </div>
+    
   </body>
 </html>