Mercurial > repos > jjohnson > opencontact

annotate OpenContact.xml @ 0:d163dd7e68b5 draft

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author jjohnson
date Thu, 16 May 2019 11:27:07 -0400
parents
children 3de332f0a26f
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1 <tool id="OpenContact" name="Open Contact" version="1.1.0" profile="16.01">
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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 <!-- Use until PQR datatype available -->
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15 <param name="proteinA" type="data" format="pdb" label="Protein A"/>
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16 <!-- -->
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17 <!-- Use when PQR datatype available
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18 <param name="proteinA" type="data" format="pdb,pqr" label="Protein A"/>
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19 -->
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20 <!-- Use until PDB chain_ids metadata -->
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21 <param name="proteinA_chain" type="text" value="" label="Protein A chain" >
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22 <validator type="regex" message="">[A-Z]</validator>
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23 </param>
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24 <!-- -->
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25 <!-- Use when PDB chain_ids metadata available
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26 <param name="proteinA_chain" type="select" label="Protein A chain" >
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27 <options>
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28 <filter type="data_meta" ref="proteinA" key="chain_ids" />
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29 </options>
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30 </param>
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31 -->
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32 <!-- Use until PQR datatype available -->
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33 <param name="proteinB" type="data" format="pdb" label="Protein B"
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34 help="This can be the same as Protein A for intra-protein interactions"/>
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35 <!-- -->
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36 <!-- Use when PQR datatype available -->
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37 <param name="proteinB" type="data" format="pdb,pqr" label="Protein B"
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38 help="This can be the same as Protein A for intra-protein interactions"/>
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39 <!-- -->
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40 <!-- Use until PDB chain_ids metadata -->
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41 <param name="proteinB_chain" type="text" value="" label="Protein B chain" >
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42 <validator type="regex" message="">[A-Z]</validator>
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43 </param>
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44 <!-- -->
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45 <!-- Use when PDB chain_ids metadata available
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46 <param name="proteinB_chain" type="select" label="Protein B chain" >
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47 <options>
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48 <filter type="data_meta" ref="proteinB" key="chain_ids" />
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49 </options>
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50 </param>
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51 -->
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52 <param name="output_choices" type="select" multiple="true" display="checkboxes" label="Select Outputs" >
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53 <option value="fineab_pdb" selected="true">fineab.pdb</option>
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54 <option value="coarseab_pdb" selected="true">coarseab.pdb</option>
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55 <option value="finedata_tsv" selected="true">finedata.tsv</option>
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56 <option value="coarsedata_tsv" selected="true">coarsedata.tsv</option>
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57 <option value="finedata_txt">finedata.txt</option>
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58 <option value="coarsedata_txt">coarsedata.txt</option>
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59 </param>
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60 </inputs>
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61 <outputs>
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62 <data name="coarsedata" format="txt" label="${tool.name} on ${on_string} coarsedata.txt"
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63 from_work_dir="coarsedata.txt">
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64 <filter>'coarsedata_txt' in output_choices</filter>
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65 </data>
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66 <data name="finedata" format="txt" label="${tool.name} on ${on_string} finedata.txt"
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67 from_work_dir="finedata.txt">
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68 <filter>'finedata_txt' in output_choices</filter>
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69 </data>
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70 <data name="coarsedata" format="tabular" label="${tool.name} on ${on_string} coarsedata.tsv"
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71 from_work_dir="coarsedata.tsv">
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72 <filter>'coarsedata_tsv' in output_choices</filter>
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73 <actions>
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74 <action name="column_names" type="metadata" default="ResA,ResNumA,AtomA,AtomNumA,ResB,ResNumB,AtomB,AtomNumB,RRS,UCOUL,UL" />
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75 </actions>
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76 </data>
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77 <data name="finedata" format="tabular" label="${tool.name} on ${on_string} finedata.tsv"
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78 from_work_dir="finedata.tsv">
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79 <filter>'finedata_tsv' in output_choices</filter>
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80 <actions>
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81 <action name="column_names" type="metadata" default="ResA,ResNumA,AtomA,AtomNumA,ResB,ResNumB,AtomB,AtomNumB,RRS,UCOUL,UL" />
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82 </actions>
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83 </data>
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84 <data name="coarseab" format="pdb" label="${tool.name} on ${on_string} coarseab.pdb"
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85 from_work_dir="coarseab.pdb">
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86 <filter>'coarseab_pdb' in output_choices</filter>
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87 </data>
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88 <data name="fineab" format="pdb" label="${tool.name} on ${on_string} fineab.pdb"
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89 from_work_dir="fineab.pdb">
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90 <filter>'fineab_pdb' in output_choices</filter>
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91 </data>
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92 </outputs>
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93 <tests>
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94 <test>
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95 <param name="proteinA" ftype="pdb" value="1AIK.pdb"/>
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96 <param name="proteinA_chain" value="C"/>
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97 <param name="proteinB" ftype="pdb" value="1AIK.pdb"/>
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98 <param name="proteinB_chain" value="N"/>
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99 <output name="coarseab" file="coarseab.pdb"/>
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100 <output name="fineab" file="fineab.pdb"/>
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101 </test>
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102 </tests>
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103 <help><![CDATA[
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104 **OpenContact**
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105 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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106
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107 **OpenContactCLI** is a python script that executes that OpenContact algorithm.
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108
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109 **Inputs**
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110 ::
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111
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112 Two PDB files and the chain ID of each PDB file that you wish to ananlyze.
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113
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114
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115 **Outputs**
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116 ::
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117
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118 coarseab.pdb
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119 fineab.pdb
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120 coarsedata.tsv
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121 finedata.tsv
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122
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123
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124 OpenContactCLI
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125 usage: OpenContactCLI [-h] -a PROTA -b PROTB -A PROTA_CHAIN -B PROTB_CHAIN [-t]
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126
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127 arguments:
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128
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129 -h, --help show this help message and exit
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130 -a PROTA, --protA PROTA
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131 Path to proteinA.pdb
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132 -b PROTB, --protB PROTB
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133 Path to proteinB.pdb
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134 -A PROTA_CHAIN, --protA_chain PROTA_CHAIN
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135 proteinA chain
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136 -B PROTB_CHAIN, --protB_chain PROTB_CHAIN
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137 proteinB chain
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138 -t, --tabular Create tab separated map files
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139
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140 ]]></help>
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141 <citations>
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142 <citation type="doi">10.1002%2Fprot.24592</citation>
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143 </citations>
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144 </tool>