|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="IDEvaluator" name="IDEvaluator" version="1.12.0">
|
|
|
3 <description>Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value.</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">IDEvaluator</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>IDEvaluator
|
|
|
11
|
|
|
12 -in ${param_in}
|
|
|
13 -out ${param_out}
|
|
|
14 -out_type ${param_out_type}
|
|
|
15 -out_csv ${param_out_csv}
|
|
|
16 -q_min ${param_q_min}
|
|
|
17 -q_max ${param_q_max}
|
|
|
18 -threads \${GALAXY_SLOTS:-24}
|
|
|
19 ${param_use_all_hits}
|
|
|
20 -algorithm:image:height ${param_height}
|
|
|
21 -algorithm:image:width ${param_width}
|
|
|
22 </command>
|
|
|
23 <inputs>
|
|
|
24 <param name="param_in" type="data" format="idXML" optional="True" size="20" label="Input file(s)" help="(-in)"/>
|
|
|
25 <param name="param_out_type" type="select" optional="True" label="The image format. Set this if you want to force a format not reflected by the 'out' filename." help="(-out_type)">
|
|
|
26 <option value="png">png</option>
|
|
|
27 <option value="jpg">jpg</option>
|
|
|
28 <option value="svg">svg</option>
|
|
|
29 </param>
|
|
|
30 <param name="param_q_min" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimal q-value in plot." help="(-q_min)"/>
|
|
|
31 <param name="param_q_max" type="float" min="0.0" max="1.0" optional="True" value="0.4" label="Maximal q-value in plot." help="(-q_max)"/>
|
|
|
32 <param name="param_use_all_hits" type="boolean" truevalue="-algorithm:fdr:use_all_hits true" falsevalue="-algorithm:fdr:use_all_hits false" checked="false" optional="True" label="If 'true' not only the first hit, but all are used (peptides only)" help="(-use_all_hits)"/>
|
|
|
33 <param name="param_height" type="integer" value="800" label="Height of raster images (e.g., PNG)." help="(-height)"/>
|
|
|
34 <param name="param_width" type="integer" value="1024" label="Width of raster images (e.g., PNG)." help="(-width)"/>
|
|
|
35 </inputs>
|
|
|
36 <outputs>
|
|
|
37 <data name="param_out" label="Output file (if given, no GUI will be displayed)" format="svg">
|
|
|
38 <change_format>
|
|
|
39 <when input="param_out_type" value="png" format="png"/>
|
|
|
40 <when input="param_out_type" value="jpg" format="jpg"/>
|
|
|
41 </change_format>
|
|
|
42 </data>
|
|
|
43 <data name="param_out_csv" label="Optional output of points as table for manual post-processing." format="tabular"/>
|
|
|
44 </outputs>
|
|
|
45 <help>**What it does**
|
|
|
46
|
|
|
47 Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value.
|
|
|
48
|
|
|
49
|
|
|
50 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDEvaluator.html
|
|
|
51
|
|
|
52 @REFERENCES@
|
|
|
53 </help>
|
|
|
54 </tool>
|
