1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
|
<HTML>
<HEAD>
<TITLE>QCShrinker</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
<A href="index.html">Home</A> ·
<A href="classes.html">Classes</A> ·
<A href="annotated.html">Annotated Classes</A> ·
<A href="modules.html">Modules</A> ·
<A href="functions_func.html">Members</A> ·
<A href="namespaces.html">Namespaces</A> ·
<A href="pages.html">Related Pages</A>
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<!-- Generated by Doxygen 1.8.5 -->
</div><!-- top -->
<div class="header">
<div class="headertitle">
<div class="title">QCShrinker </div> </div>
</div><!--header-->
<div class="contents">
<div class="textblock"><p>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> QCShrinker <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="2"><a class="el" href="UTILS_QCMerger.html">QCMerger</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1">... </td></tr>
</table>
</center><p>If there is a lot of verbose or deprecated information in the given qcml file at <code>in</code> that can be purged.</p>
<ul>
<li><code>qp_accessions</code> A list of cv accessions that should be removed. If empty, the usual suspects will be removed.</li>
<li><code>run</code> the file that defined the run under which the qp for the attachment is aggregated as MZML file. The file is only used to extract the run name from the file name;</li>
<li><code>name</code> if no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given;</li>
</ul>
<p>Output is in qcML format (see parameter <code>out</code>) which can be viewed directly in a modern browser (chromium, firefox).</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
QCShrinker -- This application is used to remove the verbose table attachments from a qcml file that are not
needed anymore, e.g. for a final report.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
QCShrinker <options>
Options (mandatory options marked with '*'):
-in <file>* Input qcml file (valid formats: 'qcML')
-qp_accessions <names> A list of cv accessions that should be removed. If empty, the usual suspects will
be removed!
-name <string> The name of the target run or set that contains the requested quality parameter.
-run <file> The file from which the name of the target run that contains the requested quality
parameter is taken. This overrides the name parameter! (valid formats: 'mzML')
-out <file>* Output extended/reduced qcML file (valid formats: 'qcML')
Common UTIL options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
<div class="legend">
<b>Legend:</b><br>
<div class="item item_required">required parameter</div>
<div class="item item_advanced">advanced parameter</div>
</div>
<div class="node"><span class="node_name">+QCShrinker</span><span class="node_description">This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'QCShrinker'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">Input qcml file</span><span class="item_tags">input file</span><span class="item_restrictions">*.qcML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">qp_accessions</span><span class="item_value">[]</span>
<span class="item_description">A list of cv accessions that should be removed. If empty, the usual suspects will be removed!</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">name</span><span class="item_value"></span>
<span class="item_description">The name of the target run or set that contains the requested quality parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">run</span><span class="item_value"></span>
<span class="item_description">The file from which the name of the target run that contains the requested quality parameter is taken. This overrides the name parameter!</span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">Output extended/reduced qcML file</span><span class="item_tags">output file</span><span class="item_restrictions">*.qcML</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div></div>
</div></div><!-- contents -->
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<TABLE width="100%" border="0">
<TR>
<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>
|
