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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: [Preparation]-->
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4 <tool id="ExtractProteinChains" name="ExtractProteinChains" version="1.1.0">
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5 <description>separate all chains of a pdb file into separate pdb files</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ExtractProteinChains</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="stdio"/>
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11 <expand macro="requirements"/>
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12 <command>ExtractProteinChains
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13
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14 #if $param_pdb:
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15 -pdb $param_pdb
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16 #end if
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17 #if $param_chain_id:
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18 -chain_id "$param_chain_id"
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19 #end if
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20 #if $param_o:
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21 -o $param_o
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22 #end if
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23 #if $adv_opts.adv_opts_selector=='advanced':
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24 #if $adv_opts.param_o_id:
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25 -o_id "$adv_opts.param_o_id"
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26 #end if
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27 #if $adv_opts.param_o_dir:
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28 -o_dir "$adv_opts.param_o_dir"
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29 #end if
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30 #end if
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31 </command>
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32 <inputs>
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33 <param name="param_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file" help="(-pdb) "/>
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34 <param name="param_chain_id" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="chain to extract" help="(-chain_id) ">
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35 <sanitizer>
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36 <valid initial="string.printable">
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37 <remove value="'"/>
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38 <remove value="""/>
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39 </valid>
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40 </sanitizer>
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41 </param>
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42 <expand macro="advanced_options">
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43 <param name="param_o_id" type="text" size="30" value="$o.id" label="output id" help="(-o_id) ">
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44 <sanitizer>
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45 <valid initial="string.printable">
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46 <remove value="'"/>
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47 <remove value="""/>
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48 </valid>
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49 </sanitizer>
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50 </param>
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51 <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last solution" help="(-o_dir) ">
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52 <sanitizer>
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53 <valid initial="string.printable">
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54 <remove value="'"/>
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55 <remove value="""/>
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56 </valid>
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57 </sanitizer>
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58 </param>
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59 </expand>
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60 </inputs>
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61 <outputs>
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62 <data name="param_o" format="pdb"/>
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63 </outputs>
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64 <help>This tool splits a pdb file into its chains.
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65
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66 </help>
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67 </tool>
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