diff OpenContact.xml @ 0:d163dd7e68b5 draft

planemo upload commit cc4319cfe5715ecd2d692df8ed2476ca7539a1aa-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenContact.xml	Thu May 16 11:27:07 2019 -0400
@@ -0,0 +1,144 @@
+<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>