comparison OpenContact.xml @ 0:d163dd7e68b5 draft

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0:d163dd7e68b5

<tool id="OpenContact" name="Open Contact" version="1.1.0" profile="16.01">
    <description>contact mapping for protein-protein interaction</description>
    <requirements>
        <requirement type="package" version="1.1">opencontactcli</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        OpenContactCLI --protA '$proteinA' --protA_chain $proteinA_chain 
                    --protB '$proteinB' --protB_chain $proteinB_chain
        #if str($output_choices).find('_tsv') > 0: 
            --tabular
        #end if
    ]]></command>
    <inputs>
        <!--  Use until PQR datatype available -->
        <param name="proteinA" type="data" format="pdb" label="Protein A"/>
        <!-- -->
        <!--  Use when PQR datatype available  
        <param name="proteinA" type="data" format="pdb,pqr" label="Protein A"/>
        -->
        <!--  Use until PDB chain_ids metadata -->
        <param name="proteinA_chain" type="text" value="" label="Protein A chain" >
            <validator type="regex" message="">[A-Z]</validator>
        </param>
        <!-- -->
        <!-- Use when PDB chain_ids metadata available 
        <param name="proteinA_chain" type="select" label="Protein A chain" >
            <options>
                <filter type="data_meta" ref="proteinA" key="chain_ids" />
            </options>
        </param>
        -->
        <!--  Use until PQR datatype available  -->
        <param name="proteinB" type="data" format="pdb" label="Protein B" 
            help="This can be the same as Protein A for intra-protein interactions"/>
        <!-- -->
        <!--  Use when PQR datatype available -->
        <param name="proteinB" type="data" format="pdb,pqr" label="Protein B" 
            help="This can be the same as Protein A for intra-protein interactions"/>
        <!-- -->
        <!--  Use until PDB chain_ids metadata -->
        <param name="proteinB_chain" type="text" value="" label="Protein B chain" >
            <validator type="regex" message="">[A-Z]</validator>
        </param>
        <!-- -->
        <!-- Use when PDB chain_ids metadata available 
        <param name="proteinB_chain" type="select" label="Protein B chain" >
            <options>
                <filter type="data_meta" ref="proteinB" key="chain_ids" />
            </options>
        </param>
        -->
        <param name="output_choices" type="select" multiple="true" display="checkboxes" label="Select Outputs" >
            <option value="fineab_pdb" selected="true">fineab.pdb</option>
            <option value="coarseab_pdb" selected="true">coarseab.pdb</option>
            <option value="finedata_tsv" selected="true">finedata.tsv</option>
            <option value="coarsedata_tsv" selected="true">coarsedata.tsv</option>
            <option value="finedata_txt">finedata.txt</option>
            <option value="coarsedata_txt">coarsedata.txt</option>
        </param>
    </inputs>
    <outputs>
        <data name="coarsedata" format="txt" label="${tool.name} on ${on_string} coarsedata.txt"
            from_work_dir="coarsedata.txt">
            <filter>'coarsedata_txt' in output_choices</filter>
        </data>
        <data name="finedata" format="txt" label="${tool.name} on ${on_string} finedata.txt"
            from_work_dir="finedata.txt">
            <filter>'finedata_txt' in output_choices</filter>
        </data>
        <data name="coarsedata" format="tabular" label="${tool.name} on ${on_string} coarsedata.tsv"
            from_work_dir="coarsedata.tsv">
            <filter>'coarsedata_tsv' in output_choices</filter>
            <actions>
                <action name="column_names" type="metadata" default="ResA,ResNumA,AtomA,AtomNumA,ResB,ResNumB,AtomB,AtomNumB,RRS,UCOUL,UL" />
            </actions>
        </data>
        <data name="finedata" format="tabular" label="${tool.name} on ${on_string} finedata.tsv"
            from_work_dir="finedata.tsv">
            <filter>'finedata_tsv' in output_choices</filter>
            <actions>
                <action name="column_names" type="metadata" default="ResA,ResNumA,AtomA,AtomNumA,ResB,ResNumB,AtomB,AtomNumB,RRS,UCOUL,UL" />
            </actions>
        </data>
        <data name="coarseab" format="pdb" label="${tool.name} on ${on_string} coarseab.pdb"
            from_work_dir="coarseab.pdb">
            <filter>'coarseab_pdb' in output_choices</filter>
        </data>
        <data name="fineab" format="pdb" label="${tool.name} on ${on_string} fineab.pdb"
            from_work_dir="fineab.pdb">
            <filter>'fineab_pdb' in output_choices</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="proteinA" ftype="pdb" value="1AIK.pdb"/>
            <param name="proteinA_chain" value="C"/>
            <param name="proteinB" ftype="pdb" value="1AIK.pdb"/>
            <param name="proteinB_chain" value="N"/>
            <output name="coarseab" file="coarseab.pdb"/>
            <output name="fineab" file="fineab.pdb"/>
        </test>
    </tests>
    <help><![CDATA[
**OpenContact**
The OpenContact algorithm provides screened or parsed protein interaction files based on specified criteria for interatomic separation distances and interatomic potential interactions.

**OpenContactCLI** is a python script that executes that OpenContact algorithm.

**Inputs**
::

   Two PDB files and the chain ID of each PDB file that you wish to ananlyze.


**Outputs**
::

    coarseab.pdb
    fineab.pdb
    coarsedata.tsv
    finedata.tsv


OpenContactCLI
usage: OpenContactCLI [-h] -a PROTA -b PROTB -A PROTA_CHAIN -B PROTB_CHAIN [-t]

arguments:

  -h, --help            show this help message and exit
  -a PROTA, --protA PROTA
                        Path to proteinA.pdb
  -b PROTB, --protB PROTB
                        Path to proteinB.pdb
  -A PROTA_CHAIN, --protA_chain PROTA_CHAIN
                        proteinA chain
  -B PROTB_CHAIN, --protB_chain PROTB_CHAIN
                        proteinB chain
  -t, --tabular         Create tab separated map files

    ]]></help>
    <citations>
        <citation type="doi">10.1002%2Fprot.24592</citation>
    </citations>
</tool>