Mercurial > repos > galaxyp > openms_qcembedder

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