Mercurial > repos > galaxyp > openms_qcshrinker

annotate QCShrinker.xml @ 3:91a44fe1c588 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d4b74e94ddabaccec6b1c5f9540d074c39207600
author galaxyp
date Sat, 28 Oct 2017 05:29:03 -0400
parents ad69b52388aa
children b186ae098994
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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="QCShrinker" name="QCShrinker" version="2.2.0">
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5 <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.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">QCShrinker</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>QCShrinker
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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
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19 #if $rep_param_qp_accessions:
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20 -qp_accessions
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21 #for token in $rep_param_qp_accessions:
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22 #if " " in str(token):
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23 "$token.param_qp_accessions"
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24 #else
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25 $token.param_qp_accessions
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26 #end if
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27 #end for
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28 #end if
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29 #if $param_name:
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30 -name "$param_name"
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31 #end if
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32 #if $param_run:
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33 -run $param_run
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34 #end if
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35 #if $param_out:
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36 -out $param_out
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37 #end if
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38 #if $adv_opts.adv_opts_selector=='advanced':
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39 #if $adv_opts.param_force:
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40 -force
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41 #end if
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42 #end if
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43 </command>
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44 <inputs>
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45 <param name="param_in" type="data" format="qcml" optional="False" label="Input qcml file" help="(-in) "/>
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46 <repeat name="rep_param_qp_accessions" min="0" max="1" title="param_qp_accessions">
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47 <param name="param_qp_accessions" type="text" size="30" label="A list of cv accessions that should be removed" help="(-qp_accessions) If empty, the usual suspects will be removed!">
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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 </repeat>
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56 <param name="param_name" type="text" size="30" label="The name of the target run or set that contains the requested quality paramete" help="(-name) ">
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57 <sanitizer>
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58 <valid initial="string.printable">
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59 <remove value="'"/>
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60 <remove value="&quot;"/>
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61 </valid>
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62 </sanitizer>
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63 </param>
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64 <param name="param_run" type="data" format="mzml" optional="True" label="The file from which the name of the target run that contains the requested quality parameter is taken" help="(-run) This overrides the name parameter!"/>
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65 <expand macro="advanced_options">
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66 <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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67 </expand>
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68 </inputs>
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69 <outputs>
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70 <data name="param_out" format="qcml"/>
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71 </outputs>
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72 <help>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.
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73
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74
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75 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCShrinker.html</help>
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76 </tool>