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changeset 7:882f2f20028b draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 608d9e59a0d2dcf85a037968ddb2c61137fb9bce
author prog
date Sun, 09 Apr 2017 10:44:21 -0400
parents b8f70d8216b3
children 0f079ad77bdf
files README.md lcmsmatching.xml test-data/filedb-small-mz-match-html-output.html test-data/filedb-small-mz-match-output.tsv test-data/filedb-small-mz-match-peaks-output.tsv
diffstat 5 files changed, 6 insertions(+), 434 deletions(-) [+]
line wrap: on
line diff
--- a/README.md	Mon Mar 27 06:27:29 2017 -0400
+++ b/README.md	Sun Apr 09 10:44:21 2017 -0400
@@ -32,6 +32,10 @@
 
 ## Updates
 
+### 3.3.1
+
+   * Correct a bug while trying to connect to Peakforest for getting the list of chromatographic columns.
+
 ### 3.3.0
 
    * The file database (in-house) field names are now presented in individual choice lists instead of a single text box where you had to insert a very long keys/values string.
--- a/lcmsmatching.xml	Mon Mar 27 06:27:29 2017 -0400
+++ b/lcmsmatching.xml	Sun Apr 09 10:44:21 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="lcmsmatching" name="LC/MS matching" version="3.3.0" profile="16.01">
+<tool id="lcmsmatching" name="LC/MS matching" version="3.3.1" profile="16.01">
 
 	<description>Annotation of MS peaks using matching on a spectra database.</description>
 
@@ -121,7 +121,7 @@
 
 				<param name="dbtoken" label="Peakforest security token" type="text" size="32" value="" refresh_on_change="true" help="If you do not have yet a Peakforest token, go to Peakforest website and request one from your account."/>
 
-				<param name="dbfields" type="text" size="32" value="" hidden="true"/>
+				<param name="dbchromcolfield" type="text" size="32" value="" hidden="true"/>
 			</when>
 		</conditional>
 
--- a/test-data/filedb-small-mz-match-html-output.html	Mon Mar 27 06:27:29 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,370 +0,0 @@
-<html>
-	<header>
-		<meta charset="UTF-8"/>
-		<title>LC/MS matching results</title>
-		<style>
-			table, th, td { border-collapse: collapse; }
-			table, th { border: 1px solid black; }
-			td { border-left: 1px solid black; border-right: 1px solid black; }
-			th, td { padding: 5px; }
-			th { background-color: LightBlue; }
-			tr:nth-child(even) { background-color: LemonChiffon; }
-			tr:nth-child(odd) { background-color: LightGreen; }
-		</style>
-	</header>
-	<body>
-		<h1>LC/MS matching</h1>
-		<h2>Parameters</h2>
-		<ul>
-			<li>Mode = pos.</li>
-			<li>M/Z precision = 5.</li>
-			<li>M/Z shift = 0.</li>
-			<li>Precursor match = no.</li>
-		</ul>
-		<h2>Results</h2>
-		<h3>Matched peaks</h3>
-		<table>
-			<tr>
-				<th>mz</th>
-				<th>compoundid</th>
-				<th>msmode</th>
-				<th>mztheo</th>
-				<th>peakcomp</th>
-				<th>peakattr</th>
-				<th>compoundcomp</th>
-				<th>compoundmass</th>
-				<th>fullnames</th>
-			</tr>
-			<tr>
-				<td>80.04959</td>
-				<td>U761</td>
-				<td>POS</td>
-				<td>80.04948</td>
-				<td>P9Z5W46 O0</td>
-				<td>[(M+H)-(NHCO)]+</td>
-				<td>J16L6M62O</td>
-				<td>122.048</td>
-				<td>Coquelicol;Paquerettol</td>
-			</tr>
-			<tr>
-				<td>82.04819</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>83.01344</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>84.05585</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>87.05536</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>89.50682</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>90.97681</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>92.98093</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>94.57331</td>
-				<td>A10</td>
-				<td>POS</td>
-				<td>94.57331</td>
-				<td>P93Z8W419 O2</td>
-				<td>[(M+2H)+(CH3CN)]++</td>
-				<td>J114L6M62O2</td>
-				<td>146.1055</td>
-				<td>Blablaine</td>
-			</tr>
-			<tr>
-				<td>97.07603</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>99.54296</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>101.0709</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>102.0663</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>102.2845</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>104.0034</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>104.5318</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>105.4461</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>105.7271</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>106.0231</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>106.24</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>106.5116</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>106.763</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>106.9815</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>107.2424</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>107.4569</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>107.6885</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>107.9273</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>108.1576</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>109.0777</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-			<tr>
-				<td>110.0599</td>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-				<td/>
-			</tr>
-		</table>
-	</body>
-</html>
--- a/test-data/filedb-small-mz-match-output.tsv	Mon Mar 27 06:27:29 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-"mz"	"compoundid"	"msmode"	"mztheo"	"peakcomp"	"peakattr"	"compoundcomp"	"compoundmass"	"fullnames"
-80.04959021	"U761"	"POS"	"80.049475"	"P9Z5W46 O0"	"[(M+H)-(NHCO)]+"	"J16L6M62O"	"122.04801"	"Coquelicol;Paquerettol"
-82.04819461	NA	NA	NA	NA	NA	NA	NA	NA
-83.01343941	NA	NA	NA	NA	NA	NA	NA	NA
-84.05585475	NA	NA	NA	NA	NA	NA	NA	NA
-87.05536392	NA	NA	NA	NA	NA	NA	NA	NA
-89.50682004	NA	NA	NA	NA	NA	NA	NA	NA
-90.97680734	NA	NA	NA	NA	NA	NA	NA	NA
-92.98092987	NA	NA	NA	NA	NA	NA	NA	NA
-94.57331384	"A10"	"POS"	"94.5733145"	"P93Z8W419 O2"	"[(M+2H)+(CH3CN)]++"	"J114L6M62O2"	"146.10553"	"Blablaine"
-97.07602789	NA	NA	NA	NA	NA	NA	NA	NA
-99.5429594	NA	NA	NA	NA	NA	NA	NA	NA
-101.0708987	NA	NA	NA	NA	NA	NA	NA	NA
-102.066292	NA	NA	NA	NA	NA	NA	NA	NA
-102.2845376	NA	NA	NA	NA	NA	NA	NA	NA
-104.0034256	NA	NA	NA	NA	NA	NA	NA	NA
-104.5317528	NA	NA	NA	NA	NA	NA	NA	NA
-105.4460999	NA	NA	NA	NA	NA	NA	NA	NA
-105.7271343	NA	NA	NA	NA	NA	NA	NA	NA
-106.0231437	NA	NA	NA	NA	NA	NA	NA	NA
-106.2399954	NA	NA	NA	NA	NA	NA	NA	NA
-106.5116177	NA	NA	NA	NA	NA	NA	NA	NA
-106.7629705	NA	NA	NA	NA	NA	NA	NA	NA
-106.9814579	NA	NA	NA	NA	NA	NA	NA	NA
-107.2424051	NA	NA	NA	NA	NA	NA	NA	NA
-107.4569385	NA	NA	NA	NA	NA	NA	NA	NA
-107.6884734	NA	NA	NA	NA	NA	NA	NA	NA
-107.9272908	NA	NA	NA	NA	NA	NA	NA	NA
-108.1575604	NA	NA	NA	NA	NA	NA	NA	NA
-109.0777249	NA	NA	NA	NA	NA	NA	NA	NA
-110.0599023	NA	NA	NA	NA	NA	NA	NA	NA
--- a/test-data/filedb-small-mz-match-peaks-output.tsv	Mon Mar 27 06:27:29 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-"mz"	"compoundid"	"msmode"	"mztheo"	"peakcomp"	"peakattr"	"compoundcomp"	"compoundmass"	"fullnames"
-80.04959021	"U761"	"POS"	80.049475	"P9Z5W46 O0"	"[(M+H)-(NHCO)]+"	"J16L6M62O"	122.04801	"Coquelicol;Paquerettol"
-82.04819461	NA	NA	NA	NA	NA	NA	NA	NA
-83.01343941	NA	NA	NA	NA	NA	NA	NA	NA
-84.05585475	NA	NA	NA	NA	NA	NA	NA	NA
-87.05536392	NA	NA	NA	NA	NA	NA	NA	NA
-89.50682004	NA	NA	NA	NA	NA	NA	NA	NA
-90.97680734	NA	NA	NA	NA	NA	NA	NA	NA
-92.98092987	NA	NA	NA	NA	NA	NA	NA	NA
-94.57331384	"A10"	"POS"	94.5733145	"P93Z8W419 O2"	"[(M+2H)+(CH3CN)]++"	"J114L6M62O2"	146.10553	"Blablaine"
-97.07602789	NA	NA	NA	NA	NA	NA	NA	NA
-99.5429594	NA	NA	NA	NA	NA	NA	NA	NA
-101.0708987	NA	NA	NA	NA	NA	NA	NA	NA
-102.066292	NA	NA	NA	NA	NA	NA	NA	NA
-102.2845376	NA	NA	NA	NA	NA	NA	NA	NA
-104.0034256	NA	NA	NA	NA	NA	NA	NA	NA
-104.5317528	NA	NA	NA	NA	NA	NA	NA	NA
-105.4460999	NA	NA	NA	NA	NA	NA	NA	NA
-105.7271343	NA	NA	NA	NA	NA	NA	NA	NA
-106.0231437	NA	NA	NA	NA	NA	NA	NA	NA
-106.2399954	NA	NA	NA	NA	NA	NA	NA	NA
-106.5116177	NA	NA	NA	NA	NA	NA	NA	NA
-106.7629705	NA	NA	NA	NA	NA	NA	NA	NA
-106.9814579	NA	NA	NA	NA	NA	NA	NA	NA
-107.2424051	NA	NA	NA	NA	NA	NA	NA	NA
-107.4569385	NA	NA	NA	NA	NA	NA	NA	NA
-107.6884734	NA	NA	NA	NA	NA	NA	NA	NA
-107.9272908	NA	NA	NA	NA	NA	NA	NA	NA
-108.1575604	NA	NA	NA	NA	NA	NA	NA	NA
-109.0777249	NA	NA	NA	NA	NA	NA	NA	NA
-110.0599023	NA	NA	NA	NA	NA	NA	NA	NA