Mercurial > repos > dfornika > blast_report

changeset 1:a56a5519d60a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit bf63225facccd1b6fcf39681ee5fe0bc887b1695-dirty
author dfornika
date Wed, 11 Sep 2019 23:32:18 -0400
parents 18b097eb1a51
children cf3e9a68d558
files blast_report.py blast_report.xml blast_report_bins.loc.sample blast_report_bins.xml.sample templates/template1.tmpl templates/template2.tmpl
diffstat 5 files changed, 251 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/blast_report.xml	Tue Sep 10 12:51:57 2019 -0400
+++ b/blast_report.xml	Wed Sep 11 23:32:18 2019 -0400
@@ -29,7 +29,7 @@
         <param name="filter_pident" type="integer" min="90" max="100" value="97" label="Minimum percentage identity"/>
         <param name="filter_kws" type="text" size="50" label="Comma-separated list of description keyword filters" value="bovine,clone,environmental,swine,uncultivated,uncultured,unidentified"/>
         <param name="bins" type="select" label="Database bins" multiple="true" display="checkboxes">
-            <options from_file="bccdc_blast_bins.loc">
+            <options from_data_table="blast_report_bins">
                 <column name="value" index="1"/>
                 <column name="name" index="0"/>
             </options>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast_report_bins.loc.sample	Wed Sep 11 23:32:18 2019 -0400
@@ -0,0 +1,7 @@
+# Expect three columns, tab separated, as follows:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - path (folder name containing the Kraken DB)
+#
+# e.g.
+# rdp<tab>RDP<tab>/path/to/bins/rdp.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast_report_bins.xml.sample	Wed Sep 11 23:32:18 2019 -0400
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of BLAST Report bins in the required format -->
+    <table name="blast_report_bins" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/blast_report_bins.loc" />
+    </table>
+</tables>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/template1.tmpl	Wed Sep 11 23:32:18 2019 -0400
@@ -0,0 +1,108 @@
+#silent import time
+#set $display_m = 20
+#set $header = '<tr class="header"><th>Accession</th><th>Description</th><th>Score</th><th>% Coverage</th><th>% Identity</th></tr>'
+<html>
+	<head>
+		<style>
+			body {
+				font-size:0.75em;
+			}
+			table, tr {
+				width: 100%;
+			}
+			table {
+				border-collapse: collapse;
+				border: 1px solid black;
+			}
+			tr.header {
+				background-color: lightgrey;
+			}
+			th {
+				border: 1px solid black;
+			}
+			td {
+				border-left: 1px solid black;
+				border-right: 1px solid black;
+				border-bottom: 1px dashed grey;
+			}
+			td.descr {
+				font-size: 80%;
+			}
+			h3 {
+				page-break-before: always;
+				color: blue;
+			}
+			h3.first {
+				page-break-before: avoid;
+			}
+			span.super {
+				color: navy;
+				font-size: 75%;
+				vertical-align: top;
+			}
+		</style>
+		<script>
+			function toggle(id){
+				var element = document.getElementById(id)
+				console.log(id)
+				if (element.style.display == 'none') {
+					//console.log(element.tagName);
+					if (element.tagName == 'TBODY') element.style.display = 'table-row-group';
+					else if (element.tagName == 'TD') element.style.display = 'table-cell';
+					else element.style.display = 'block';
+				} else {
+					element.style.display = 'none';
+				}
+			}
+		</script>
+	</head>
+	<body>
+		#set $q = 0
+		#for $query in $queries
+			#set $bin_symbols = dict([($bin,$i) for $i, $bin in enumerate($query.bins, 1)])
+			#set $m = 0
+			<h3 id="${query.query_id}" #if $q == 0 then'class="first"' else '' #>$query.query_id</h3>
+			<br/>
+			<table id="${query.query_id}_matches">
+			#if len($query.matches) == 0:
+				<tr class="header"><th colspan="5">No matches to report</th></tr>
+			</table>
+			#else:
+			$header
+			#for $match in $query.matches:
+				#if $m == $display_m
+				<tbody id="${query.query_id}_extra" style="display:none">
+				#end if
+				<tr>
+					<td>$match.subject_acc <span class="super">#echo ', '.join(sorted([str($bin_symbols[$bin]) for $bin in $match.bins]))#</span></td>
+					<td class="descr">$match.subject_descr</td>
+					<td>$match.score</td>
+					<td>$match.p_cov</td>
+					<td>$match.p_ident</td>
+				</tr>
+			#set $m += 1
+			#end for
+			#if $m >= $display_m
+			</tbody>
+				<td id="${query.query_id}_show" align="center" colspan="6" >Displaying ${display_m}/$m matches. <a href="#${query.query_id}_extra" onclick="toggle('${query.query_id}_extra'); toggle('${query.query_id}_show'); toggle('${query.query_id}_hide');">Show the remaining results.</a></td>
+				<td id="${query.query_id}_hide" align="center" colspan="6" style="display:none"><a href="#${query.query_id}" onclick="toggle('${query.query_id}_extra'); toggle('${query.query_id}_show'); toggle('${query.query_id}_hide');">Hide the last #echo $m - $display_m # results.</a></td>
+			<tr>
+			</tr>
+			#end if
+			</table>
+			#if len($bin_symbols) > 0:
+			<p>#echo ', '.join(['<span class="super">%s</span> %s'%($bin_symbols[$bin],$bin) for $bin in $query.bins])#</p>
+			#end if
+			#end if
+			#if $query.pident_filtered > 0:
+			<p>$query.pident_filtered results filtered by % Identity.</p>
+			#end if
+			#if $query.kw_filtered > 0:
+			<p>$query.kw_filtered results filtered by description keywords: #echo ', '.join(list(["%s matches to '%s'" % (str($query.kw_filtered_breakdown[$kw]),$kw) for $kw in $query.kw_filtered_breakdown])) #.</p>
+			#end if
+			<p>Report produced on #echo time.strftime("%d/%m/%Y") #.</p>
+			<hr noshade size="1" color="blue">
+		#set $q += 1
+		#end for
+	</body>
+</html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/template2.tmpl	Wed Sep 11 23:32:18 2019 -0400
@@ -0,0 +1,127 @@
+#silent import time
+#set $display_m = 20
+#set $header = '<tr class="header"><th>Accession</th><th>Description</th><th>Score</th><th>% Coverage</th><th>% Identity</th></tr>'
+<html>
+	<head>
+		<style>
+			body {
+				font-size:0.75em;
+			}
+			table, tr {
+				width: 100%;
+			}
+			table {
+				border-collapse: collapse;
+				border: 1px solid black;
+			}
+			tr.header {
+				background-color: lightgrey;
+			}
+			th {
+				border: 1px solid black;
+			}
+			td {
+				border-left: 1px solid black;
+				border-right: 1px solid black;
+				border-bottom: 1px dashed grey;
+			}
+			td.descr {
+				font-size: 80%;
+			}
+			h3 {
+				page-break-before: always;
+				color: blue;
+			}
+			h3.first {
+				page-break-before: avoid;
+			}
+			span.super {
+				color: navy;
+				font-size: 75%;
+				vertical-align: top;
+			}
+		</style>
+		<script>
+			function toggle(id){
+				var element = document.getElementById(id)
+				console.log(id)
+				if (element.style.display == 'none') {
+					//console.log(element.tagName);
+					if (element.tagName == 'TBODY') element.style.display = 'table-row-group';
+					else if (element.tagName == 'TD') element.style.display = 'table-cell';
+					else element.style.display = 'block';
+				} else {
+					element.style.display = 'none';
+				}
+			}
+		</script>
+	</head>
+	<body>
+		#set $q = 0
+		#for $query in $queries
+			#set $bin_symbols = dict([($bin,$i) for $i, $bin in enumerate($query.bins, 1)])
+			#set $m = 0
+			<h3 id="${query.query_id}" #if $q == 0 then'class="first"' else '' #>$query.query_id</h3>
+			<br/>
+			<table id="${query.query_id}_matches">
+			#set $num_of_euzby = -1
+			#if len($query.matches) == 0:
+				<tr class="header"><th colspan="5">No matches to report</th></tr>
+			</table>
+			#else:
+			$header
+			#try
+			#set $priority = $query.bins['Euzby']
+			#set $front = []
+			#for $i in reversed($priority)
+			#silent $front.append($query.matches.pop($i))
+			#end for
+			#set $num_of_euzby = len($front)
+			#silent $front.reverse()
+			#silent $front.extend($query.matches)
+			#set $query.matches = $front
+			#except
+			#pass
+			#end try
+			#for $match in $query.matches:
+				#if $m == $display_m
+				<tbody id="${query.query_id}_extra" style="display:none">
+				#end if
+				##if $m>0 and set($match.bins)!=set($query.matches[m-1].bins)
+				##put an empty line to separate Euzby records from other records
+				#if $m==$num_of_euzby and $m>0
+				<tr><td align="center" colspan="6">&nbsp;</td></tr>
+				#end if
+				<tr>
+					<td>$match.subject_acc <span class="super">#echo ', '.join(sorted([str($bin_symbols[$bin]) for $bin in $match.bins]))#</span></td>
+					<td class="descr">$match.subject_descr</td>
+					<td>$match.score</td>
+					<td>$match.p_cov</td>
+					<td>$match.p_ident</td>
+				</tr>
+			#set $m += 1
+			#end for
+			#if $m >= $display_m
+			</tbody>
+				<td id="${query.query_id}_show" align="center" colspan="6" >Displaying ${display_m}/$m matches. <a href="#${query.query_id}_extra" onclick="toggle('${query.query_id}_extra'); toggle('${query.query_id}_show'); toggle('${query.query_id}_hide');">Show the remaining results.</a></td>
+				<td id="${query.query_id}_hide" align="center" colspan="6" style="display:none"><a href="#${query.query_id}" onclick="toggle('${query.query_id}_extra'); toggle('${query.query_id}_show'); toggle('${query.query_id}_hide');">Hide the last #echo $m - $display_m # results.</a></td>
+			<tr>
+			</tr>
+			#end if
+			</table>
+			#if len($bin_symbols) > 0:
+			<p>#echo ', '.join(['<span class="super">%s</span> %s'%($bin_symbols[$bin],$bin) for $bin in $query.bins])#</p>
+			#end if
+			#end if
+			#if $query.pident_filtered > 0:
+			<p>$query.pident_filtered results filtered by % Identity.</p>
+			#end if
+			#if $query.kw_filtered > 0:
+			<p>$query.kw_filtered results filtered by description keywords: #echo ', '.join(list(["%s matches to '%s'" % (str($query.kw_filtered_breakdown[$kw]),$kw) for $kw in $query.kw_filtered_breakdown])) #.</p>
+			#end if
+			<p>Report produced on #echo time.strftime("%d/%m/%Y") #.</p>
+			<hr noshade size="1" color="blue">
+		#set $q += 1
+		#end for
+	</body>
+</html>