Mercurial > repos > galaxyp > openms_qcshrinker
comparison QCShrinker.xml @ 0:2092c98a7c43 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 12:54:11 -0500 |
| parents | |
| children | ad69b52388aa |
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| -1:000000000000 | 0:2092c98a7c43 |
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| 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="QCShrinker" name="QCShrinker" version="2.1.0"> | |
| 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> | |
| 6 <macros> | |
| 7 <token name="@EXECUTABLE@">QCShrinker</token> | |
| 8 <import>macros.xml</import> | |
| 9 </macros> | |
| 10 <expand macro="references"/> | |
| 11 <expand macro="stdio"/> | |
| 12 <expand macro="requirements"/> | |
| 13 <command>QCShrinker | |
| 14 | |
| 15 #if $param_in: | |
| 16 -in $param_in | |
| 17 #end if | |
| 18 | |
| 19 #if $rep_param_qp_accessions: | |
| 20 -qp_accessions | |
| 21 #for token in $rep_param_qp_accessions: | |
| 22 #if " " in str(token): | |
| 23 "$token.param_qp_accessions" | |
| 24 #else | |
| 25 $token.param_qp_accessions | |
| 26 #end if | |
| 27 #end for | |
| 28 #end if | |
| 29 #if $param_name: | |
| 30 -name "$param_name" | |
| 31 #end if | |
| 32 #if $param_run: | |
| 33 -run $param_run | |
| 34 #end if | |
| 35 #if $param_out: | |
| 36 -out $param_out | |
| 37 #end if | |
| 38 #if $adv_opts.adv_opts_selector=='advanced': | |
| 39 #if $adv_opts.param_force: | |
| 40 -force | |
| 41 #end if | |
| 42 #end if | |
| 43 </command> | |
| 44 <inputs> | |
| 45 <param name="param_in" type="data" format="qcml" optional="False" label="Input qcml file" help="(-in) "/> | |
| 46 <repeat name="rep_param_qp_accessions" min="0" max="1" title="param_qp_accessions"> | |
| 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!"> | |
| 48 <sanitizer> | |
| 49 <valid initial="string.printable"> | |
| 50 <remove value="'"/> | |
| 51 <remove value="""/> | |
| 52 </valid> | |
| 53 </sanitizer> | |
| 54 </param> | |
| 55 </repeat> | |
| 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) "> | |
| 57 <sanitizer> | |
| 58 <valid initial="string.printable"> | |
| 59 <remove value="'"/> | |
| 60 <remove value="""/> | |
| 61 </valid> | |
| 62 </sanitizer> | |
| 63 </param> | |
| 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!"/> | |
| 65 <expand macro="advanced_options"> | |
| 66 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
| 67 </expand> | |
| 68 </inputs> | |
| 69 <outputs> | |
| 70 <data name="param_out" format="qcml"/> | |
| 71 </outputs> | |
| 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. | |
| 73 | |
| 74 | |
| 75 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCShrinker.html</help> | |
| 76 </tool> |