Mercurial > repos > jjohnson > opencontact

annotate OpenContact.xml @ 2:52d76e9da089 draft default tip

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author jjohnson
date Thu, 16 May 2019 12:04:35 -0400
parents 3de332f0a26f
children
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1 <tool id="OpenContact" name="Open Contact" version="1.1.1" profile="18.09">
0
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2 <description>contact mapping for protein-protein interaction</description>
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3 <requirements>
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4 <requirement type="package" version="1.1">opencontactcli</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 OpenContactCLI --protA '$proteinA' --protA_chain $proteinA_chain
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8 --protB '$proteinB' --protB_chain $proteinB_chain
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9 #if str($output_choices).find('_tsv') > 0:
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10 --tabular
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11 #end if
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12 ]]></command>
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13 <inputs>
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14 <param name="proteinA" type="data" format="pdb,pqr" label="Protein A"/>
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15 <param name="proteinA_chain" type="select" label="Protein A chain" >
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16 <options>
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17 <filter type="data_meta" ref="proteinA" key="chain_ids" />
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18 </options>
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19 </param>
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20 <param name="proteinB" type="data" format="pdb,pqr" label="Protein B"
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21 help="This can be the same as Protein A for intra-protein interactions"/>
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22 <param name="proteinB_chain" type="select" label="Protein B chain" >
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23 <options>
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24 <filter type="data_meta" ref="proteinB" key="chain_ids" />
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25 </options>
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26 </param>
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27 <param name="output_choices" type="select" multiple="true" display="checkboxes" label="Select Outputs" >
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28 <option value="fineab_pdb" selected="true">fineab.pdb</option>
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29 <option value="coarseab_pdb" selected="true">coarseab.pdb</option>
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30 <option value="finedata_tsv" selected="true">finedata.tsv</option>
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31 <option value="coarsedata_tsv" selected="true">coarsedata.tsv</option>
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32 <option value="finedata_txt">finedata.txt</option>
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33 <option value="coarsedata_txt">coarsedata.txt</option>
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34 </param>
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35 </inputs>
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36 <outputs>
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37 <data name="coarsedata" format="txt" label="${tool.name} on ${on_string} coarsedata.txt"
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38 from_work_dir="coarsedata.txt">
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39 <filter>'coarsedata_txt' in output_choices</filter>
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40 </data>
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41 <data name="finedata" format="txt" label="${tool.name} on ${on_string} finedata.txt"
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42 from_work_dir="finedata.txt">
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43 <filter>'finedata_txt' in output_choices</filter>
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44 </data>
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45 <data name="coarsedata" format="tabular" label="${tool.name} on ${on_string} coarsedata.tsv"
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46 from_work_dir="coarsedata.tsv">
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47 <filter>'coarsedata_tsv' in output_choices</filter>
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48 <actions>
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49 <action name="column_names" type="metadata" default="ResA,ResNumA,AtomA,AtomNumA,ResB,ResNumB,AtomB,AtomNumB,RRS,UCOUL,UL" />
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50 </actions>
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51 </data>
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52 <data name="finedata" format="tabular" label="${tool.name} on ${on_string} finedata.tsv"
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53 from_work_dir="finedata.tsv">
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54 <filter>'finedata_tsv' in output_choices</filter>
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55 <actions>
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56 <action name="column_names" type="metadata" default="ResA,ResNumA,AtomA,AtomNumA,ResB,ResNumB,AtomB,AtomNumB,RRS,UCOUL,UL" />
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57 </actions>
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58 </data>
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59 <data name="coarseab" format="pdb" label="${tool.name} on ${on_string} coarseab.pdb"
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60 from_work_dir="coarseab.pdb">
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61 <filter>'coarseab_pdb' in output_choices</filter>
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62 </data>
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63 <data name="fineab" format="pdb" label="${tool.name} on ${on_string} fineab.pdb"
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64 from_work_dir="fineab.pdb">
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65 <filter>'fineab_pdb' in output_choices</filter>
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66 </data>
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67 </outputs>
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68 <tests>
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69 <test>
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70 <param name="proteinA" ftype="pdb" value="1AIK.pdb"/>
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71 <param name="proteinA_chain" value="C"/>
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72 <param name="proteinB" ftype="pdb" value="1AIK.pdb"/>
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73 <param name="proteinB_chain" value="N"/>
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74 <output name="coarseab" file="coarseab.pdb"/>
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75 <output name="fineab" file="fineab.pdb"/>
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76 </test>
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77 </tests>
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78 <help><![CDATA[
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79 **OpenContact**
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80 The OpenContact algorithm provides screened or parsed protein interaction files based on specified criteria for interatomic separation distances and interatomic potential interactions.
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81
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82 **OpenContactCLI** is a python script that executes that OpenContact algorithm.
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83
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84 **Inputs**
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85 ::
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86
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87 Two PDB files and the chain ID of each PDB file that you wish to ananlyze.
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88
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89
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90 **Outputs**
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91 ::
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92
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93 coarseab.pdb
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94 fineab.pdb
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95 coarsedata.tsv
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96 finedata.tsv
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97
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98
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99 OpenContactCLI
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100 usage: OpenContactCLI [-h] -a PROTA -b PROTB -A PROTA_CHAIN -B PROTB_CHAIN [-t]
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101
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102 arguments:
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103
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104 -h, --help show this help message and exit
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105 -a PROTA, --protA PROTA
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106 Path to proteinA.pdb
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107 -b PROTB, --protB PROTB
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108 Path to proteinB.pdb
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109 -A PROTA_CHAIN, --protA_chain PROTA_CHAIN
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110 proteinA chain
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111 -B PROTB_CHAIN, --protB_chain PROTB_CHAIN
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112 proteinB chain
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113 -t, --tabular Create tab separated map files
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114
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115 ]]></help>
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116 <citations>
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117 <citation type="doi">10.1002%2Fprot.24592</citation>
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118 </citations>
d163dd7e68b5 planemo upload commit cc4319cfe5715ecd2d692df8ed2476ca7539a1aa-dirty
jjohnson
parents:
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119 </tool>