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comparison QCEmbedder.xml @ 0:66aa3156aeb5 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:52:50 -0500
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children 401b56e2b31b
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-1:000000000000 0:66aa3156aeb5
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="QCEmbedder" name="QCEmbedder" version="2.1.0">
5 <description>Attaches a table or an image to a given qc parameter.</description>
6 <macros>
7 <token name="@EXECUTABLE@">QCEmbedder</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>QCEmbedder
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_qp_att_acc:
19 -qp_att_acc "$param_qp_att_acc"
20 #end if
21 #if $param_cv_acc:
22 -cv_acc "$param_cv_acc"
23 #end if
24 #if $param_run:
25 -run $param_run
26 #end if
27 #if $param_name:
28 -name "$param_name"
29 #end if
30 #if $param_plot:
31 -plot $param_plot
32 #end if
33 #if $param_table:
34 -table $param_table
35 #end if
36 #if $param_out:
37 -out $param_out
38 #end if
39 #if $adv_opts.adv_opts_selector=='advanced':
40 #if $adv_opts.param_force:
41 -force
42 #end if
43 #end if
44 </command>
45 <inputs>
46 <param name="param_in" type="data" format="qcml" optional="True" label="Input qcml file" help="(-in) "/>
47 <param name="param_qp_att_acc" type="text" size="30" label="Defines the qp cv accession of the qp to which the table/image is attached" help="(-qp_att_acc) ">
48 <sanitizer>
49 <valid initial="string.printable">
50 <remove value="'"/>
51 <remove value="&quot;"/>
52 </valid>
53 </sanitizer>
54 </param>
55 <param name="param_cv_acc" type="text" size="30" label="Defines the cv accession of the attachment" help="(-cv_acc) ">
56 <sanitizer>
57 <valid initial="string.printable">
58 <remove value="'"/>
59 <remove value="&quot;"/>
60 </valid>
61 </sanitizer>
62 </param>
63 <param name="param_run" type="data" format="mzml" optional="True" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="(-run) The file is only used to extract the run name from the file name"/>
64 <param name="param_name" type="text" size="30" label="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" help="(-name) ">
65 <sanitizer>
66 <valid initial="string.printable">
67 <remove value="'"/>
68 <remove value="&quot;"/>
69 </valid>
70 </sanitizer>
71 </param>
72 <param name="param_plot" type="data" format="" optional="True" label="If a plot image is to be attached to a qp, this has to be specified here" help="(-plot) "/>
73 <param name="param_table" type="data" format="tabular" optional="True" label="If a table is to be attached to a qp, this has to be specified here" help="(-table) "/>
74 <expand macro="advanced_options">
75 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
76 </expand>
77 </inputs>
78 <outputs>
79 <data name="param_out" format="qcml"/>
80 </outputs>
81 <help>Attaches a table or an image to a given qc parameter.
82
83
84 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCEmbedder.html</help>
85 </tool>