From commits-noreply@bitbucket.org Fri Feb 25 14:58:45 2011
From: Bitbucket <commits-noreply@bitbucket.org>
To: galaxy-commits@lists.galaxyproject.org
Subject: [galaxy-commits] commit/galaxy-central: kanwei: Update test-data
	files for meme 4.6.0
Date: Fri, 25 Feb 2011 19:58:40 +0000
Message-ID: <20110225195840.23045.78088@bitbucket02.managed.contegix.com>
MIME-Version: 1.0
Content-Type: multipart/mixed; boundary="===============0785695880878396854=="

--===============0785695880878396854==
Content-Type: text/plain; charset="utf-8"
Content-Transfer-Encoding: quoted-printable

1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/e448ba0e8843/
changeset:   r5129:e448ba0e8843
user:        kanwei
date:        2011-02-25 20:58:35
summary:     Update test-data files for meme 4.6.0
affected #:  4 files (2.8 KB)

--- a/test-data/meme/meme/meme_output_html_1.html	Fri Feb 25 13:35:27 2011 -0=
500
+++ b/test-data/meme/meme/meme_output_html_1.html	Fri Feb 25 14:58:35 2011 -0=
500
@@ -4,6 +4,8 @@
 <meta http-equiv=3D"Content-Type" content=3D"text/html; charset=3DUTF-8"><ti=
tle>MEME</title><style type=3D"text/css">
+   =20
+    /* START INCLUDED FILE "meme.css" */
         /* The following is the content of meme.css */
         body { background-color:white; font-size: 12px; font-family: Verdana=
, Arial, Helvetica, sans-serif;}
=20
@@ -13,6 +15,7 @@
           padding: 0px;
           width: 12px;
           height: 13px;
+          cursor: pointer;
           background-image: url("help.gif");
           background-image: url("data:image/png;base64,iVBORw0KGgoAAAANSUhEU=
gAAAAwAAAANAQMAAACn5x0BAAAAAXNSR0IArs4c6QAAAAZQTFRFAAAAnp6eqp814gAAAAF0Uk5TAE=
Dm2GYAAAABYktHRACIBR1IAAAACXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH2gMJBQgGYqhNZQA=
AACZJREFUCNdj+P+BoUGAoV+AYeYEEGoWYGgTYGgRAAm2gRGQ8f8DAOnhC2lYnqs6AAAAAElFTkSu=
QmCC");
         }
@@ -123,8 +126,12 @@
           padding:0px 10px;
         }
=20
+    /* END INCLUDED FILE "meme.css" */
+   =20
   </style><script type=3D"text/javascript">
+   =20
+    /* START INCLUDED FILE "motif_logo.js" */
     //=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
     // start Alphabet object
     //=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
@@ -337,7 +344,9 @@
     //=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
     // start Pspm object
     //=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
-    function Pspm(pssm, name) {
+    function Pspm(pssm, name, ltrim, rtrim) {
+      if (ltrim =3D=3D=3D undefined) ltrim =3D 0;
+      if (rtrim =3D=3D=3D undefined) rtrim =3D 0;
       //variable prototype
       this.alph_length =3D 0;
       this.motif_length =3D 0;
@@ -345,6 +354,8 @@
       this.name =3D (typeof name =3D=3D "string" ? name : "");
       this.nsites =3D 0;
       this.evalue =3D 0;
+      this.ltrim =3D ltrim;
+      this.rtrim =3D rtrim;
       //function prototype
       this.copy =3D Pspm_copy;
       this.reverse_complement =3D Pspm_reverse_complement;
@@ -352,10 +363,11 @@
       this.get_stack_ic =3D Pspm_get_stack_ic;
       this.get_motif_length =3D Pspm_get_motif_length;
       this.get_alph_length =3D Pspm_get_alph_length;
+      this.get_left_trim =3D Pspm_get_left_trim;
+      this.get_right_trim =3D Pspm_get_right_trim;
       this.toString =3D Pspm_to_string;
       //construct
       var pspm_header =3D /letter-probability matrix:\s+alength=3D\s+(\d+)\s=
+w=3D\s+(\d+)(\s+nsites=3D\s+(\S+))?(\s+E=3D\s+(\S+))?\s*/;
-      var is_prob =3D /^((1(\.0+)?)|(0(\.\d+)?))$/;
       var is_empty =3D /^\s*$/;
       var lines =3D pssm.split(/\s*\n\s*/);
       var read_pssm =3D false;
@@ -392,11 +404,14 @@
           if (!parts.hasOwnProperty(part_index) || parts[part_index] =3D=3D=
=3D undefined) continue;
          =20
           var prob =3D parts[part_index];
-          if (!is_prob.test(prob)) continue;
           if (col_num >=3D this.alph_length) {
             throw "TOO_MANY_COLS";
           }
           this.pspm[line_num][col_num] =3D (+prob);
+          //check the probability is within bounds
+          if (this.pspm[line_num][col_num] > 1 || this.pspm[line_num][col_nu=
m] < 0) {
+            throw "NUM_NOT_PROB";
+          }
           col_num++;
         }
         if (col_num !=3D this.alph_length) {
@@ -417,6 +432,11 @@
       //so far only a shallow copy, need to copy everything
       clone.alph_length =3D (0+this.alph_length);
       clone.motif_length =3D (0+this.motif_length);
+      clone.name =3D (""+this.name);
+      clone.nsites =3D (0+this.nsites);
+      clone.evalue =3D (0+this.evalue);
+      clone.ltrim =3D (0+this.ltrim);
+      clone.rtrim =3D (0+this.rtrim);
       clone.pspm =3D new Array(this.motif_length);
       for (row =3D 0; row < this.motif_length; row++) {
         clone.pspm[row] =3D new Array(this.alph_length);
@@ -460,6 +480,10 @@
         row[c_index] =3D row[g_index];
         row[g_index] =3D temp;
       }
+      //swap triming
+      var temp_trim =3D this.ltrim;
+      this.ltrim =3D this.rtrim;
+      this.rtrim =3D temp_trim;
       //note that ambigs are ignored because they don't effect motifs
       return this; //allow function chaining...
     }
@@ -515,6 +539,14 @@
       return this.alph_length;
     }
=20
+    function Pspm_get_left_trim() {
+      return this.ltrim;
+    }
+
+    function Pspm_get_right_trim() {
+      return this.rtrim;
+    }
+
     function Pspm_to_string() {
       var str =3D "";
       for (row_index in this.pspm) {
@@ -1036,6 +1068,62 @@
         pos =3D pos - sym_height;
       }
     }
+   =20
+    function draw_dashed_line(ctx, pattern, start, x1, y1, x2, y2) {
+        var x, y, len, i;
+        var dx =3D x2 - x1;
+        var dy =3D y2 - y1;
+        var tlen =3D Math.pow(dx*dx + dy*dy, 0.5);
+        var theta =3D Math.atan2(dy,dx);
+        var mulx =3D Math.cos(theta);
+        var muly =3D Math.sin(theta);
+        var lx =3D [];
+        var ly =3D [];
+        for (i =3D 0; i < pattern; ++i) {
+          lx.push(pattern[i] * mulx);
+          ly.push(pattern[i] * muly);
+        }
+        i =3D start;
+        x =3D x1;
+        y =3D y1;
+        len =3D 0;
+        ctx.beginPath();
+        while (len + pattern[i] < tlen) {
+          ctx.moveTo(x, y);
+          x +=3D lx[i];
+          y +=3D ly[i];
+          ctx.lineTo(x, y);
+          len +=3D pattern[i];
+          i =3D (i + 1) % pattern.length;
+          x +=3D lx[i];
+          y +=3D ly[i];
+          len +=3D pattern[i];
+          i =3D (i + 1) % pattern.length;
+        }
+        if (len < tlen) {
+          ctx.moveTo(x, y);
+          x +=3D mulx * (tlen - len);
+          y +=3D muly * (tlen - len);
+          ctx.lineTo(x, y);
+        }
+        ctx.stroke();
+    }
+
+    function draw_trim_background(ctx, metrics, pspm, offset) {
+      var lwidth =3D metrics.stack_width * pspm.get_left_trim();
+      var rwidth =3D metrics.stack_width * pspm.get_right_trim();
+      var mwidth =3D metrics.stack_width * pspm.get_motif_length();
+      var rstart =3D mwidth - rwidth;
+      ctx.save();//s8
+      ctx.translate(offset * metrics.stack_width, 0);
+      ctx.fillStyle =3D "rgb(240, 240, 240)";
+      if (pspm.get_left_trim() > 0) ctx.fillRect(0, 0, lwidth, metrics.stack=
_height);
+      if (pspm.get_right_trim() > 0) ctx.fillRect(rstart, 0, rwidth, metrics=
.stack_height);
+      ctx.fillStyle =3D "rgb(51, 51, 51)";
+      if (pspm.get_left_trim() > 0) draw_dashed_line(ctx, [3], 0, lwidth-0.5=
, 0, lwidth-0.5,  metrics.stack_height);
+      if (pspm.get_right_trim() > 0) draw_dashed_line(ctx, [3], 0, rstart+0.=
5, 0, rstart+0.5,  metrics.stack_height);
+      ctx.restore();//s8
+    }
=20
     function draw_logo_on_canvas(logo, canvas, show_names, scale) {
       var draw_name =3D (typeof show_names =3D=3D "boolean" ? show_names : (=
logo.get_rows() > 1));
@@ -1089,6 +1177,10 @@
         //translate across past the scale
         ctx.translate(metrics.y_label_height + metrics.y_label_spacer +=20
             metrics.y_num_width + metrics.y_tic_width, 0);
+        //draw the trimming background
+        if (pspm.get_left_trim() > 0 || pspm.get_right_trim() > 0) {
+          draw_trim_background(ctx, metrics, pspm, offset);
+        }
         //draw letters
         ctx.translate(0, metrics.y_num_height / 2);
         for (var col_index =3D 0; col_index < logo.get_columns(); col_index+=
+) {
@@ -1211,15 +1303,8 @@
       element.parentNode.replaceChild(canvas, element);
     }
=20
-    //example code for creating a logo
-    //function do_load() {
-    //  var alphabet =3D new Alphabet(document.getElementById("alphabet").va=
lue, document.getElementById("bgfreq").value);
-    //  var pspm =3D new Pspm(document.getElementById("pspm1").value);
-    //  var pspm_rc =3D pspm.copy().reverse_complement(alphabet);
-    //  draw_logo(pspm, alphabet, "Motif 1", "logo1");
-    //  draw_logo(pspm_rc, alphabet, "Motif 1 Reverse Complement", "logo_rc1=
");
-    //}
-
+    /* END INCLUDED FILE "motif_logo.js" */
+   =20
  =20
         function setup() {
           var motif_count =3D 1;
@@ -1377,15 +1462,15 @@
         }
       </script></head>
-<body onload=3D"javascript:setup()"><form enctype=3D"application/x-www-form-=
urlencoded" method=3D"post" target=3D"_new" action=3D"http://dan/meme_request=
.cgi">
+<body onload=3D"javascript:setup()"><form enctype=3D"application/x-www-form-=
urlencoded" method=3D"post" target=3D"_new" action=3D"http://straub/meme/cgi-=
bin/meme_request.cgi"><!--+++++++++++++++++++++++START DATA++++++++++++++++++=
+++++++++++++++++++-->
-<input type=3D"hidden" name=3D"version" value=3D"MEME version 4.5.0">
+<input type=3D"hidden" name=3D"version" value=3D"MEME version 4.6.0"><input =
type=3D"hidden" name=3D"alphabet" id=3D"alphabet" value=3D"ACDEFGHIKLMNPQRSTV=
WY"><input type=3D"hidden" name=3D"strands" value=3D"none"><input type=3D"hid=
den" name=3D"bgfreq" id=3D"bgfreq" value=3D"A 0.291 C 0.229 D 0.001 E 0.001 F=
 0.001 G 0.255 H 0.001 I 0.001 K 0.001=20
 L 0.001 M 0.001 N 0.001 P 0.001 Q 0.001 R 0.001 S 0.001 T 0.215 V 0.001=20
 W 0.001 Y 0.001">
-<input type=3D"hidden" name=3D"name" value=3D"dan.dat">
+<input type=3D"hidden" name=3D"name" value=3D"dataset_3.dat"><input type=3D"=
hidden" name=3D"combinedblock" value=3D"
 chr21_19617074_19617124_+ 1.22e-03 1 50 1 39 3.06e-05=20
 chr21_26934381_26934431_+ 2.21e-03 1 50 1 27 5.52e-05=20
@@ -2179,12 +2264,12 @@
 </tbody></table></div>
-<p>Time 1.6 secs.</p>
+<p>Time 2.1 secs.</p></div><div class=3D"bar"><div style=3D"text-align:right=
;"><a href=3D"#top_buttons">Top</a></div><div class=3D"subsection">
-<a name=3D"version"></a><h5>MEME version</h5>4.5.0 (Release date: Thu Oct 14=
 08:44:28 EST 2010)
+<a name=3D"version"></a><h5>MEME version</h5>4.6.0 (Release date: Thu Jan 20=
 14:06:48 PST 2011)
       </div><div class=3D"subsection"><a name=3D"reference"></a><h5>Referenc=
e</h5>
@@ -2196,7 +2281,7 @@
       </div><a name=3D"sequences"></a><a href=3D"javascript:showHidden('trai=
ningseq')" id=3D"trainingseq_activator">show training set...</a><div class=3D=
"subsection" id=3D"trainingseq_data" style=3D"display:none;"><h5>Training set=
:</h5>
-        Datafile =3D dan.dat<br>
+        Datafile =3D dataset_3.dat<br>
         Alphabet =3D ACDEFGHIKLMNPQRSTVWY<br><table><col><col>
@@ -2387,19 +2472,19 @@
 </div><a href=3D"javascript:hideShown('trainingseq')" style=3D"display:none;=
" id=3D"trainingseq_deactivator">hide training set...</a><div class=3D"subsec=
tion"><a name=3D"command"></a><h5>Command line summary</h5>
-<textarea rows=3D"1" style=3D"width:100%;" readonly>meme dan.dat -o /dataset=
_dan_files -nostatus </textarea><br>
+<textarea rows=3D"1" style=3D"width:100%;" readonly>meme dataset_3.dat -o da=
taset_4_files -nostatus </textarea><br>
         Letter frequencies in dataset<br><div style=3D"margin-left:25px;">A:=
=C2=A00.294=C2=A0=C2=A0=C2=A0C:=C2=A00.231=C2=A0=C2=A0=C2=A0D:=C2=A00.000=C2=
=A0=C2=A0=C2=A0E:=C2=A00.000=C2=A0=C2=A0=C2=A0F:=C2=A00.000=C2=A0=C2=A0=C2=A0=
G:=C2=A00.257=C2=A0=C2=A0=C2=A0H:=C2=A00.000=C2=A0=C2=A0=C2=A0I:=C2=A00.000=
=C2=A0=C2=A0=C2=A0K:=C2=A00.000=C2=A0=C2=A0=C2=A0L:=C2=A00.000=C2=A0=C2=A0=C2=
=A0M:=C2=A00.000=C2=A0=C2=A0=C2=A0N:=C2=A00.000=C2=A0=C2=A0=C2=A0P:=C2=A00.00=
0=C2=A0=C2=A0=C2=A0Q:=C2=A00.000=C2=A0=C2=A0=C2=A0R:=C2=A00.000=C2=A0=C2=A0=
=C2=A0S:=C2=A00.000=C2=A0=C2=A0=C2=A0T:=C2=A00.217=C2=A0=C2=A0=C2=A0V:=C2=A00=
.000=C2=A0=C2=A0=C2=A0W:=C2=A00.000=C2=A0=C2=A0=C2=A0Y:=C2=A00.000</div><br>
         Background letter frequencies (from dataset with add-one prior appli=
ed):<br><div style=3D"margin-left:25px;">A:=C2=A00.291=C2=A0=C2=A0=C2=A0C:=C2=
=A00.229=C2=A0=C2=A0=C2=A0D:=C2=A00.001=C2=A0=C2=A0=C2=A0E:=C2=A00.001=C2=A0=
=C2=A0=C2=A0F:=C2=A00.001=C2=A0=C2=A0=C2=A0G:=C2=A00.255=C2=A0=C2=A0=C2=A0H:=
=C2=A00.001=C2=A0=C2=A0=C2=A0I:=C2=A00.001=C2=A0=C2=A0=C2=A0K:=C2=A00.001=C2=
=A0=C2=A0=C2=A0L:=C2=A00.001=C2=A0=C2=A0=C2=A0M:=C2=A00.001=C2=A0=C2=A0=C2=A0=
N:=C2=A00.001=C2=A0=C2=A0=C2=A0P:=C2=A00.001=C2=A0=C2=A0=C2=A0Q:=C2=A00.001=
=C2=A0=C2=A0=C2=A0R:=C2=A00.001=C2=A0=C2=A0=C2=A0S:=C2=A00.001=C2=A0=C2=A0=C2=
=A0T:=C2=A00.215=C2=A0=C2=A0=C2=A0V:=C2=A00.001=C2=A0=C2=A0=C2=A0W:=C2=A00.00=
1=C2=A0=C2=A0=C2=A0Y:=C2=A00.001</div><br></div><div class=3D"subsection">
-<a name=3D"stopped"></a><h5>Stopping Reason</h5>Stopped because nmotifs =3D =
1 reached. Program ran on <i>dan</i>.
+<a name=3D"stopped"></a><h5>Stopping Reason</h5>Stopped because nmotifs =3D =
1 reached. Program ran on <i>scofield</i>.
       </div><a href=3D"javascript:showHidden('model')" id=3D"model_activator=
">show model parameters...</a><div class=3D"subsection" id=3D"model_data" sty=
le=3D"display:none;"><h5>Model parameters</h5><textarea style=3D"width:100%;"=
 rows=3D"28" readonly>
-host                  =3D dan
+host                  =3D scofield
 type                  =3D zoops
 nmotifs               =3D 1
 evalue_threshold      =3D inf


--- a/test-data/meme/meme/meme_output_txt_1.txt	Fri Feb 25 13:35:27 2011 -0500
+++ b/test-data/meme/meme/meme_output_txt_1.txt	Fri Feb 25 14:58:35 2011 -0500
@@ -1,7 +1,7 @@
 ****************************************************************************=
****
 MEME - Motif discovery tool
 ****************************************************************************=
****
-MEME version 4.5.0 (Release date: Thu Oct 14 08:44:28 EST 2010)
+MEME version 4.6.0 (Release date: Thu Jan 20 14:06:48 PST 2011)
=20
 For further information on how to interpret these results or to get
 a copy of the MEME software please access http://meme.nbcr.net.
@@ -28,7 +28,7 @@
 ****************************************************************************=
****
 TRAINING SET
 ****************************************************************************=
****
-DATAFILE=3D dan.dat
+DATAFILE=3D dataset_3.dat
 ALPHABET=3D ACDEFGHIKLMNPQRSTVWY
 Sequence name            Weight Length  Sequence name            Weight Leng=
th =20
 -------------            ------ ------  -------------            ------ ----=
-- =20
@@ -55,7 +55,7 @@
 This information can also be useful in the event you wish to report a
 problem with the MEME software.
=20
-command: meme dan.dat -o dan/dataset_dan_files -nostatus=20
+command: meme dataset_3.dat -o dataset_4_files -nostatus=20
=20
 model:  mod=3D         zoops    nmotifs=3D         1    evt=3D           inf
 object function=3D  E-value of product of p-values
@@ -267,7 +267,7 @@
=20
=20
=20
-Time  1.56 secs.
+Time  2.13 secs.
=20
 ****************************************************************************=
****
=20
@@ -320,6 +320,6 @@
 Stopped because nmotifs =3D 1 reached.
 ****************************************************************************=
****
=20
-CPU: dan
+CPU: scofield
=20
 ****************************************************************************=
****


--- a/test-data/meme/meme/meme_output_xml_1.xml	Fri Feb 25 13:35:27 2011 -0500
+++ b/test-data/meme/meme/meme_output_xml_1.xml	Fri Feb 25 14:58:35 2011 -0500
@@ -157,8 +157,8 @@
=20
 ]><!-- Begin document body -->
-<MEME version=3D"4.5.0" release=3D"Thu Oct 14 08:44:28 EST 2010">
-<training_set datafile=3D"/dan_110.dat" length=3D"30">
+<MEME version=3D"4.6.0" release=3D"Thu Jan 20 14:06:48 PST 2011">
+<training_set datafile=3D"dataset_3.dat" length=3D"30"><alphabet id=3D"amino=
-acid" length=3D"20"><letter id=3D"letter_A" symbol=3D"A"/><letter id=3D"lett=
er_C" symbol=3D"C"/>
@@ -183,6 +183,8 @@
 </alphabet><ambigs><letter id=3D"letter_B" symbol=3D"B"/>
+<letter id=3D"letter_J" symbol=3D"J"/>
+<letter id=3D"letter_O" symbol=3D"O"/><letter id=3D"letter_U" symbol=3D"U"/>=
<letter id=3D"letter_X" symbol=3D"X"/><letter id=3D"letter_Z" symbol=3D"Z"/>
@@ -245,8 +247,8 @@
 </letter_frequencies></training_set><model>
-<command_line>meme /dan.dat -o /dataset_dan_files -nostatus </command_line>
-<host>dan</host>
+<command_line>meme dataset_3.dat -o dataset_4_files -nostatus </command_line>
+<host>scofield</host><type>zoops</type><nmotifs>1</nmotifs><evalue_threshold=
>inf</evalue_threshold>
@@ -300,7 +302,7 @@
 </background_frequencies></model><motifs>
-<motif id=3D"motif_1" name=3D"1" width=3D"11" sites=3D"25" ic=3D"40.0" re=3D=
"13.8" llr=3D"239" e_value=3D"2.4e-011" bayes_threshold=3D"5.33554" elapsed_t=
ime=3D"1.563760">
+<motif id=3D"motif_1" name=3D"1" width=3D"11" sites=3D"25" ic=3D"40.0" re=3D=
"13.8" llr=3D"239" e_value=3D"2.4e-011" bayes_threshold=3D"5.33554" elapsed_t=
ime=3D"2.128133"><scores><alphabet_matrix><alphabet_array>


--- a/tools/meme/meme.xml	Fri Feb 25 13:35:27 2011 -0500
+++ b/tools/meme/meme.xml	Fri Feb 25 14:58:35 2011 -0500
@@ -319,7 +319,7 @@
       <param name=3D"input1" value=3D"meme_input_1.fasta" ftype=3D"fasta" db=
key=3D"hg19"/><param name=3D"options_type_selector" value=3D"basic"/><param n=
ame=3D"non_commercial_use" value=3D"True"/>
-      <output name=3D"html_outfile" file=3D"meme/meme/meme_output_html_1.htm=
l" lines_diff=3D"14"/>
+      <output name=3D"html_outfile" file=3D"meme/meme/meme_output_html_1.htm=
l" lines_diff=3D"12"/><output name=3D"txt_outfile" file=3D"meme/meme/meme_out=
put_txt_1.txt" lines_diff=3D"12"/><output name=3D"xml_outfile" file=3D"meme/m=
eme/meme_output_xml_1.xml" lines_diff=3D"8"/></test>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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