February 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Suppress most logging for cufflinks and cuffdiff as the logging can generate output that is incompatible with UTF-8 format used by database.
by Bitbucket 27 Feb '11

27 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9bcf6ac08839/ changeset: r5136:9bcf6ac08839 user: jgoecks date: 2011-02-27 20:48:23 summary: Suppress most logging for cufflinks and cuffdiff as the logging can generate output that is incompatible with UTF-8 format used by database. affected #: 2 files (136 bytes) --- a/tools/ngs_rna/cuffdiff_wrapper.py Sat Feb 26 13:12:44 2011 -0500 +++ b/tools/ngs_rna/cuffdiff_wrapper.py Sun Feb 27 14:48:23 2011 -0500 @@ -135,8 +135,8 @@ # Build command. - # Base. - cmd = "cuffdiff" + # Base; always use quiet mode to avoid problems with storing log output. + cmd = "cuffdiff -q" # Add options. if options.inner_dist_std_dev: --- a/tools/ngs_rna/cufflinks_wrapper.py Sat Feb 26 13:12:44 2011 -0500 +++ b/tools/ngs_rna/cufflinks_wrapper.py Sun Feb 27 14:48:23 2011 -0500 @@ -84,8 +84,8 @@ # Build command. - # Base. - cmd = "cufflinks" + # Base; always use quiet mode to avoid problems with storing log output. + cmd = "cufflinks -q" # Add options. if options.inner_dist_std_dev: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Add mosaik index location file to buildbot setup.
by Bitbucket 26 Feb '11

26 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e58da3d454f2/ changeset: r5135:e58da3d454f2 user: natefoo date: 2011-02-26 19:12:44 summary: Add mosaik index location file to buildbot setup. affected #: 1 file (39 bytes) --- a/buildbot_setup.sh Sat Feb 26 10:53:50 2011 -0500 +++ b/buildbot_setup.sh Sat Feb 26 13:12:44 2011 -0500 @@ -48,6 +48,7 @@ /galaxy/data/location/maf_index.loc /galaxy/data/location/maf_pairwise.loc /galaxy/data/location/microbes/microbial_data.loc +/galaxy/data/location/mosaik_index.loc /galaxy/data/location/perm_base_index.loc /galaxy/data/location/perm_color_index.loc /galaxy/data/location/phastOdds.loc Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Basic Freebayes test added.
by Bitbucket 26 Feb '11

26 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/71c61850ea7a/ changeset: r5134:71c61850ea7a user: dannon date: 2011-02-26 16:53:50 summary: Basic Freebayes test added. affected #: 3 files (277 bytes) --- a/tools/human_genome_variation/freebayes.xml Fri Feb 25 17:53:58 2011 -0500 +++ b/tools/human_genome_variation/freebayes.xml Sat Feb 26 10:53:50 2011 -0500 @@ -112,6 +112,10 @@ </outputs><tests><test> + <param name="reference" ftype="fasta" value="mosaik_test_ref.fasta"/> + <param name="bamfile" ftype="bam" value="freebayes_in.bam"/> + <param name="source_select" value="pre_set"/> + <output name="output" ftype="vcf" file="freebayes_out.vcf" lines_diff="4"/></test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Freebayes and Mosaik updates
by Bitbucket 25 Feb '11

25 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6537337eeb50/ changeset: r5133:6537337eeb50 user: dannon date: 2011-02-25 23:53:58 summary: Freebayes and Mosaik updates affected #: 5 files (742 bytes) Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: rc: Fixed adding an external service to a request type in edit_request_type
by Bitbucket 25 Feb '11

25 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/cad3884b8729/ changeset: r5132:cad3884b8729 user: rc date: 2011-02-25 22:25:54 summary: Fixed adding an external service to a request type in edit_request_type affected #: 1 file (37 bytes) --- a/lib/galaxy/web/controllers/request_type.py Fri Feb 25 16:12:17 2011 -0500 +++ b/lib/galaxy/web/controllers/request_type.py Fri Feb 25 16:25:54 2011 -0500 @@ -244,7 +244,7 @@ sample_form_id = params.get( 'sample_form_id', 'none' ) external_service_id = params.get( 'external_service_id', 'none' ) # validate - if not name or request_form_id == 'none' or sample_form_id == 'none' or not kwd.has_key( 'state_name_0' ): + if not name or request_form_id == 'none' or sample_form_id == 'none': message = 'Enter the name, request form, sample form and at least one sample state associated with this request type.' return trans.response.send_redirect( web.url_for( controller='request_type', action=action, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: rc: Bug fix: do not show sample field widgets in the view request page
by Bitbucket 25 Feb '11

25 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/67f76a732e97/ changeset: r5131:67f76a732e97 user: rc date: 2011-02-25 22:12:17 summary: Bug fix: do not show sample field widgets in the view request page affected #: 4 files (49 bytes) --- a/templates/requests/common/add_samples.mako Fri Feb 25 15:58:13 2011 -0500 +++ b/templates/requests/common/add_samples.mako Fri Feb 25 16:12:17 2011 -0500 @@ -71,7 +71,7 @@ ## Render the other grids <% trans.sa_session.refresh( request.type.sample_form ) %> %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, adding_new_samples=True )} + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, show_saved_samples_read_only=True )} %endfor %else: <label>There are no samples.</label> --- a/templates/requests/common/common.mako Fri Feb 25 15:58:13 2011 -0500 +++ b/templates/requests/common/common.mako Fri Feb 25 16:12:17 2011 -0500 @@ -606,7 +606,7 @@ </tr></%def> -<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, displayable_sample_widgets, adding_new_samples )"> +<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, displayable_sample_widgets, show_saved_samples_read_only )"><% if not grid_name: grid_name = "Sample form layout %s" % str( grid_index ) @@ -629,7 +629,7 @@ <% trans.sa_session.refresh( request ) %> %for sample_index, sample in enumerate( displayable_sample_widgets ): <% - if not adding_new_samples or sample_index >= len( request.samples ): + if not show_saved_samples_read_only or sample_index >= len( request.samples ): display_only = False else: display_only = True --- a/templates/requests/common/edit_samples.mako Fri Feb 25 15:58:13 2011 -0500 +++ b/templates/requests/common/edit_samples.mako Fri Feb 25 16:12:17 2011 -0500 @@ -120,7 +120,7 @@ ## Render the other grids <% trans.sa_session.refresh( request.type.sample_form ) %> %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, adding_new_samples=False )} + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, show_saved_samples_read_only=False )} %endfor %else: <label>There are no samples.</label> --- a/templates/requests/common/view_request.mako Fri Feb 25 15:58:13 2011 -0500 +++ b/templates/requests/common/view_request.mako Fri Feb 25 16:12:17 2011 -0500 @@ -162,7 +162,7 @@ ## Render the other grids <% trans.sa_session.refresh( request.type.sample_form ) %> %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, adding_new_samples=False )} + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, show_saved_samples_read_only=True )} %endfor %else: There are no samples. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: rc: First pass of extract & filter VCF tools.
by Bitbucket 25 Feb '11

25 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/69338ee03d1d/ changeset: r5130:69338ee03d1d user: rc date: 2011-02-25 21:58:13 summary: First pass of extract & filter VCF tools. affected #: 6 files (22 bytes) --- a/tools/vcf_tools/annotate.xml Fri Feb 25 14:58:35 2011 -0500 +++ b/tools/vcf_tools/annotate.xml Fri Feb 25 15:58:13 2011 -0500 @@ -1,5 +1,5 @@ -<tool id="vcf_annotate" name="Annotate a VCF file" version="1.0.0"> - <description></description> +<tool id="vcf_annotate" name="Annotate" version="1.0.0"> + <description>a VCF file (dbSNP, hapmap)</description><command interpreter="python"> vcfPytools.py annotate @@ -27,7 +27,7 @@ </conditional></inputs><outputs> - <data format="vcf" name="output1" label="${tool.name} on ${on_string}" /> + <data format="vcf" name="output1" label="${tool.name} ${on_string}" /></outputs><tests><test> --- a/tools/vcf_tools/intersect.xml Fri Feb 25 14:58:35 2011 -0500 +++ b/tools/vcf_tools/intersect.xml Fri Feb 25 15:58:13 2011 -0500 @@ -1,4 +1,4 @@ -<tool id="vcf_intersect" name="Intersect VCF Files" version="1.0.0"> +<tool id="vcf_intersect" name="Intersect" version="1.0.0"><description>Generate the intersection of two VCF files</description><command interpreter="python"> vcfPytools.py Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Update test-data files for meme 4.6.0
by Bitbucket 25 Feb '11

25 Feb '11

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 -0500 +++ b/test-data/meme/meme/meme_output_html_1.html Fri Feb 25 14:58:35 2011 -0500 @@ -4,6 +4,8 @@ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>MEME</title><style type="text/css"> + + /* 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;} @@ -13,6 +15,7 @@ padding: 0px; width: 12px; height: 13px; + cursor: pointer; background-image: url("help.gif"); background-image: url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAwAAAANAQMAAACn5x0BAAAAAXNSR0IArs4c6QAAAAZQTFRFAAAAnp6eqp814gAAAAF0Uk5TAEDm2GYAAAABYktHRACIBR1IAAAACXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH2gMJBQgGYqhNZQAAACZJREFUCNdj+P+BoUGAoV+AYeYEEGoWYGgTYGgRAAm2gRGQ8f8DAOnhC2lYnqs6AAAAAElFTkSuQmCC"); } @@ -123,8 +126,12 @@ padding:0px 10px; } + /* END INCLUDED FILE "meme.css" */ + </style><script type="text/javascript"> + + /* START INCLUDED FILE "motif_logo.js" */ //====================================================================== // start Alphabet object //====================================================================== @@ -337,7 +344,9 @@ //====================================================================== // start Pspm object //====================================================================== - function Pspm(pssm, name) { + function Pspm(pssm, name, ltrim, rtrim) { + if (ltrim === undefined) ltrim = 0; + if (rtrim === undefined) rtrim = 0; //variable prototype this.alph_length = 0; this.motif_length = 0; @@ -345,6 +354,8 @@ this.name = (typeof name == "string" ? name : ""); this.nsites = 0; this.evalue = 0; + this.ltrim = ltrim; + this.rtrim = rtrim; //function prototype this.copy = Pspm_copy; this.reverse_complement = Pspm_reverse_complement; @@ -352,10 +363,11 @@ this.get_stack_ic = Pspm_get_stack_ic; this.get_motif_length = Pspm_get_motif_length; this.get_alph_length = Pspm_get_alph_length; + this.get_left_trim = Pspm_get_left_trim; + this.get_right_trim = Pspm_get_right_trim; this.toString = Pspm_to_string; //construct var pspm_header = /letter-probability matrix:\s+alength=\s+(\d+)\s+w=\s+(\d+)(\s+nsites=\s+(\S+))?(\s+E=\s+(\S+))?\s*/; - var is_prob = /^((1(\.0+)?)|(0(\.\d+)?))$/; var is_empty = /^\s*$/; var lines = pssm.split(/\s*\n\s*/); var read_pssm = false; @@ -392,11 +404,14 @@ if (!parts.hasOwnProperty(part_index) || parts[part_index] === undefined) continue; var prob = parts[part_index]; - if (!is_prob.test(prob)) continue; if (col_num >= this.alph_length) { throw "TOO_MANY_COLS"; } this.pspm[line_num][col_num] = (+prob); + //check the probability is within bounds + if (this.pspm[line_num][col_num] > 1 || this.pspm[line_num][col_num] < 0) { + throw "NUM_NOT_PROB"; + } col_num++; } if (col_num != this.alph_length) { @@ -417,6 +432,11 @@ //so far only a shallow copy, need to copy everything clone.alph_length = (0+this.alph_length); clone.motif_length = (0+this.motif_length); + clone.name = (""+this.name); + clone.nsites = (0+this.nsites); + clone.evalue = (0+this.evalue); + clone.ltrim = (0+this.ltrim); + clone.rtrim = (0+this.rtrim); clone.pspm = new Array(this.motif_length); for (row = 0; row < this.motif_length; row++) { clone.pspm[row] = new Array(this.alph_length); @@ -460,6 +480,10 @@ row[c_index] = row[g_index]; row[g_index] = temp; } + //swap triming + var temp_trim = this.ltrim; + this.ltrim = this.rtrim; + this.rtrim = 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; } + function Pspm_get_left_trim() { + return this.ltrim; + } + + function Pspm_get_right_trim() { + return this.rtrim; + } + function Pspm_to_string() { var str = ""; for (row_index in this.pspm) { @@ -1036,6 +1068,62 @@ pos = pos - sym_height; } } + + function draw_dashed_line(ctx, pattern, start, x1, y1, x2, y2) { + var x, y, len, i; + var dx = x2 - x1; + var dy = y2 - y1; + var tlen = Math.pow(dx*dx + dy*dy, 0.5); + var theta = Math.atan2(dy,dx); + var mulx = Math.cos(theta); + var muly = Math.sin(theta); + var lx = []; + var ly = []; + for (i = 0; i < pattern; ++i) { + lx.push(pattern[i] * mulx); + ly.push(pattern[i] * muly); + } + i = start; + x = x1; + y = y1; + len = 0; + ctx.beginPath(); + while (len + pattern[i] < tlen) { + ctx.moveTo(x, y); + x += lx[i]; + y += ly[i]; + ctx.lineTo(x, y); + len += pattern[i]; + i = (i + 1) % pattern.length; + x += lx[i]; + y += ly[i]; + len += pattern[i]; + i = (i + 1) % pattern.length; + } + if (len < tlen) { + ctx.moveTo(x, y); + x += mulx * (tlen - len); + y += muly * (tlen - len); + ctx.lineTo(x, y); + } + ctx.stroke(); + } + + function draw_trim_background(ctx, metrics, pspm, offset) { + var lwidth = metrics.stack_width * pspm.get_left_trim(); + var rwidth = metrics.stack_width * pspm.get_right_trim(); + var mwidth = metrics.stack_width * pspm.get_motif_length(); + var rstart = mwidth - rwidth; + ctx.save();//s8 + ctx.translate(offset * metrics.stack_width, 0); + ctx.fillStyle = "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 = "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 + } function draw_logo_on_canvas(logo, canvas, show_names, scale) { var draw_name = (typeof show_names == "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 + 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 = 0; col_index < logo.get_columns(); col_index++) { @@ -1211,15 +1303,8 @@ element.parentNode.replaceChild(canvas, element); } - //example code for creating a logo - //function do_load() { - // var alphabet = new Alphabet(document.getElementById("alphabet").value, document.getElementById("bgfreq").value); - // var pspm = new Pspm(document.getElementById("pspm1").value); - // var pspm_rc = 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" */ + function setup() { var motif_count = 1; @@ -1377,15 +1462,15 @@ } </script></head> -<body onload="javascript:setup()"><form enctype="application/x-www-form-urlencoded" method="post" target="_new" action="http://dan/meme_request.cgi"> +<body onload="javascript:setup()"><form enctype="application/x-www-form-urlencoded" method="post" target="_new" action="http://straub/meme/cgi-bin/meme_request.cgi"> -<input type="hidden" name="version" value="MEME version 4.5.0"> +<input type="hidden" name="version" value="MEME version 4.6.0"><input type="hidden" name="alphabet" id="alphabet" value="ACDEFGHIKLMNPQRSTVWY"><input type="hidden" name="strands" value="none"><input type="hidden" name="bgfreq" id="bgfreq" value="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 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 W 0.001 Y 0.001"> -<input type="hidden" name="name" value="dan.dat"> +<input type="hidden" name="name" value="dataset_3.dat"><input type="hidden" name="combinedblock" value=" chr21_19617074_19617124_+ 1.22e-03 1 50 1 39 3.06e-05 chr21_26934381_26934431_+ 2.21e-03 1 50 1 27 5.52e-05 @@ -2179,12 +2264,12 @@ </tbody></table></div> -<p>Time 1.6 secs.</p> +<p>Time 2.1 secs.</p></div><div class="bar"><div style="text-align:right;"><a href="#top_buttons">Top</a></div><div class="subsection"> -<a name="version"></a><h5>MEME version</h5>4.5.0 (Release date: Thu Oct 14 08:44:28 EST 2010) +<a name="version"></a><h5>MEME version</h5>4.6.0 (Release date: Thu Jan 20 14:06:48 PST 2011) </div><div class="subsection"><a name="reference"></a><h5>Reference</h5> @@ -2196,7 +2281,7 @@ </div><a name="sequences"></a><a href="javascript:showHidden('trainingseq')" id="trainingseq_activator">show training set...</a><div class="subsection" id="trainingseq_data" style="display:none;"><h5>Training set:</h5> - Datafile = dan.dat<br> + Datafile = dataset_3.dat<br> Alphabet = ACDEFGHIKLMNPQRSTVWY<br><table><col><col> @@ -2387,19 +2472,19 @@ </div><a href="javascript:hideShown('trainingseq')" style="display:none;" id="trainingseq_deactivator">hide training set...</a><div class="subsection"><a name="command"></a><h5>Command line summary</h5> -<textarea rows="1" style="width:100%;" readonly>meme dan.dat -o /dataset_dan_files -nostatus </textarea><br> +<textarea rows="1" style="width:100%;" readonly>meme dataset_3.dat -o dataset_4_files -nostatus </textarea><br> Letter frequencies in dataset<br><div style="margin-left:25px;">A: 0.294 C: 0.231 D: 0.000 E: 0.000 F: 0.000 G: 0.257 H: 0.000 I: 0.000 K: 0.000 L: 0.000 M: 0.000 N: 0.000 P: 0.000 Q: 0.000 R: 0.000 S: 0.000 T: 0.217 V: 0.000 W: 0.000 Y: 0.000</div><br> Background letter frequencies (from dataset with add-one prior applied):<br><div style="margin-left:25px;">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 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 W: 0.001 Y: 0.001</div><br></div><div class="subsection"> -<a name="stopped"></a><h5>Stopping Reason</h5>Stopped because nmotifs = 1 reached. Program ran on <i>dan</i>. +<a name="stopped"></a><h5>Stopping Reason</h5>Stopped because nmotifs = 1 reached. Program ran on <i>scofield</i>. </div><a href="javascript:showHidden('model')" id="model_activator">show model parameters...</a><div class="subsection" id="model_data" style="display:none;"><h5>Model parameters</h5><textarea style="width:100%;" rows="28" readonly> -host = dan +host = scofield type = zoops nmotifs = 1 evalue_threshold = 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) 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= dan.dat +DATAFILE= dataset_3.dat ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ @@ -55,7 +55,7 @@ This information can also be useful in the event you wish to report a problem with the MEME software. -command: meme dan.dat -o dan/dataset_dan_files -nostatus +command: meme dataset_3.dat -o dataset_4_files -nostatus model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values @@ -267,7 +267,7 @@ -Time 1.56 secs. +Time 2.13 secs. ******************************************************************************** @@ -320,6 +320,6 @@ Stopped because nmotifs = 1 reached. ******************************************************************************** -CPU: dan +CPU: scofield ******************************************************************************** --- 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 @@ ]> -<MEME version="4.5.0" release="Thu Oct 14 08:44:28 EST 2010"> -<training_set datafile="/dan_110.dat" length="30"> +<MEME version="4.6.0" release="Thu Jan 20 14:06:48 PST 2011"> +<training_set datafile="dataset_3.dat" length="30"><alphabet id="amino-acid" length="20"><letter id="letter_A" symbol="A"/><letter id="letter_C" symbol="C"/> @@ -183,6 +183,8 @@ </alphabet><ambigs><letter id="letter_B" symbol="B"/> +<letter id="letter_J" symbol="J"/> +<letter id="letter_O" symbol="O"/><letter id="letter_U" symbol="U"/><letter id="letter_X" symbol="X"/><letter id="letter_Z" symbol="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="motif_1" name="1" width="11" sites="25" ic="40.0" re="13.8" llr="239" e_value="2.4e-011" bayes_threshold="5.33554" elapsed_time="1.563760"> +<motif id="motif_1" name="1" width="11" sites="25" ic="40.0" re="13.8" llr="239" e_value="2.4e-011" bayes_threshold="5.33554" elapsed_time="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="input1" value="meme_input_1.fasta" ftype="fasta" dbkey="hg19"/><param name="options_type_selector" value="basic"/><param name="non_commercial_use" value="True"/> - <output name="html_outfile" file="meme/meme/meme_output_html_1.html" lines_diff="14"/> + <output name="html_outfile" file="meme/meme/meme_output_html_1.html" lines_diff="12"/><output name="txt_outfile" file="meme/meme/meme_output_txt_1.txt" lines_diff="12"/><output name="xml_outfile" file="meme/meme/meme_output_xml_1.xml" lines_diff="8"/></test> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: Typos
by Bitbucket 25 Feb '11

25 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5215215c3659/ changeset: r5128:5215215c3659 user: kanwei date: 2011-02-25 19:35:27 summary: Typos affected #: 4 files (21 bytes) --- a/tools/filters/fileGrep.xml Thu Feb 24 19:07:41 2011 -0500 +++ b/tools/filters/fileGrep.xml Fri Feb 25 13:35:27 2011 -0500 @@ -1,19 +1,19 @@ -<tool id="fileGrep1" name="Match"> - <description>a column from one Query against another Query</description> - <command>cut -f $col $input1 | grep -f - $match $input2 > $out_file1</command> - <inputs> - <param name="col" size="2" type="text" value="1" label="Match content of column"/> - <param format="tabular" name="input1" type="data" label="From Query1"/> +<tool id="fileGrep1" name="Match"> + <description>a column from one Query against another Query</description> + <command>cut -f $col $input1 | grep -f - $match $input2 > $out_file1</command> + <inputs> + <param name="col" size="2" type="text" value="1" label="Match content of column"/> + <param format="tabular" name="input1" type="data" label="From Query1"/><param format="tabular" name="input2" type="data" label="Against Query2"/> - <param name="match" type="select" label="and return rows that"> - <option value="">Match</option> - <option value="-v">Do not match</option> - </param> - </inputs> - <outputs> + <param name="match" type="select" label="and return rows that"> + <option value="">Match</option> + <option value="-v">Do not match</option> + </param> + </inputs> + <outputs><data format="input" name="out_file1" metadata_source="input2" /> - </outputs> - <help> + </outputs> + <help> This tool is based on UNIX command grep with option -f. It matches content of one query against another. For example, assume you have two queries - one that contains EST accession numbers and some other information:: AA001229 12 12 @@ -32,11 +32,11 @@ chr7 115443243 115443347 DB331869_exon_0_0_chr7_115443244_f 0 + chr7 115443347 115443373 DB331869_exon_1_0_chr7_115443348_f 0 + -Using this tool you will bne able to tell how many ESTs in Query1 are also preset in Query2 and will output this:: +Using this tool you will be able to tell how many ESTs in Query1 are also preset in Query2 and will output this:: chr7 115443239 115443802 AA001842_exon_0_0_chr7_115443240_f 0 if **Match** option is chosen. -</help> +</help></tool> \ No newline at end of file --- a/tools/ngs_rna/cuffdiff_wrapper.xml Thu Feb 24 19:07:41 2011 -0500 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Fri Feb 25 13:35:27 2011 -0500 @@ -209,7 +209,7 @@ 1. Transcript FPKM expression tracking. 2. Gene FPKM expression tracking; tracks the summed FPKM of transcripts sharing each gene_id 3. Primary transcript FPKM tracking; tracks the summed FPKM of transcripts sharing each tss_id -4. Coding sequence FPKM tracking; tracks the summed FPKM of transcripts sharing each p_id, indepedent of tss_id +4. Coding sequence FPKM tracking; tracks the summed FPKM of transcripts sharing each p_id, independent of tss_id 5. Transcript differential FPKM. 6. Gene differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each gene_id 7. Primary transcript differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each tss_id @@ -233,7 +233,7 @@ -m INT This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 45bp. -s INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp. -Q Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0. - -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not signficant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads). + -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads). --FDR FLOAT The allowed false discovery rate. The default is 0.05. --num-importance-samples INT Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000 --max-mle-iterations INT Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000 --- a/tools/ngs_rna/tophat_wrapper.xml Thu Feb 24 19:07:41 2011 -0500 +++ b/tools/ngs_rna/tophat_wrapper.xml Fri Feb 25 13:35:27 2011 -0500 @@ -25,7 +25,7 @@ ## First input file always required. --input1=$singlePaired.input1 - ## Set parms based on whether reads are single-end or paired. + ## Set params based on whether reads are single-end or paired. #if $singlePaired.sPaired == "single": --settings=$singlePaired.sParams.sSettingsType #if $singlePaired.sParams.sSettingsType == "full": @@ -171,7 +171,7 @@ <option value="full">Full parameter list</option></param><when value="preSet" /> -  + <when value="full"><param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol."><option value="fr-unstranded">FR Unstranded</option> @@ -277,7 +277,7 @@ <option value="full">Full parameter list</option></param><when value="preSet" /> -  + <when value="full"><param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol."><option value="fr-unstranded">FR Unstranded</option> @@ -435,7 +435,7 @@ <test><param name="genomeSource" value="history"/> --- a/tools/sr_mapping/lastz_wrapper.xml Thu Feb 24 19:07:41 2011 -0500 +++ b/tools/sr_mapping/lastz_wrapper.xml Fri Feb 25 13:35:27 2011 -0500 @@ -504,7 +504,7 @@ up 65 thousand --census32[=<output_file>] count and report how many times each target bas aligns, up to 4 billion - --writecapsule=<capsule_file> just write out a targegt capsule file and quit; don't + --writecapsule=<capsule_file> just write out a target capsule file and quit; don't search for seeds or perform subsequent stages --verbosity=<level> set info level (0 is minimum, 10 is everything) (default is 0) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: Only lowercase columns if starting with "c".. fixes issue where "None" was lowercased to "none". Fixes subtract_query tests
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/88a118487292/ changeset: r5127:88a118487292 user: kanwei date: 2011-02-25 01:07:41 summary: Only lowercase columns if starting with "c".. fixes issue where "None" was lowercased to "none". Fixes subtract_query tests affected #: 1 file (28 bytes) --- a/lib/galaxy/tools/parameters/basic.py Thu Feb 24 18:21:46 2011 -0500 +++ b/lib/galaxy/tools/parameters/basic.py Thu Feb 24 19:07:41 2011 -0500 @@ -845,9 +845,8 @@ removes the 'c' when entered into a workflow. """ def _strip_c( column ): - column = column.strip().lower() if column.startswith( 'c' ): - column = column[1:] + column = column.strip().lower()[1:] return column if self.multiple: #split on newline and , Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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