Mercurial > repos > guerler > springsuite

annotate spring_cross.xml @ 37:0be0af9e695d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
author guerler
date Wed, 25 Nov 2020 14:35:35 +0000
parents
children 80a4b98121b6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
37
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
1 <tool id="spring_cross" name="SPRING Cross" version="0.1.0" python_template_version="3.5" license="MIT">
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
2 <description>reference builder</description>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
3 <command detect_errors="exit_code"><![CDATA[
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
4 python3 '$__tool_directory__/spring_cross.py' -l '$list' -i '$index' -d '$database' -o '$output' -g '$log' -t temp
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
5 ]]></command>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
6 <inputs>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
7 <param format="tabular" name="list" type="data" label="PDB Chain Identifiers" help="List of PDB chains [PDB_CHAIN]."/>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
8 <param format="tabular" name="index" type="data" label="PDB Database Index" help="Database Index file (ffindex)."/>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
9 <param format="data" name="database" type="data" label="PDB Database" help="Database Data file (ffdata)."/>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
10 </inputs>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
11 <outputs>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
12 <data format="tabular" name="output" label="SPRING Cross Reference"/>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
13 <data format="txt" name="log" label="SPRING Cross Log"/>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
14 </outputs>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
15 <help><![CDATA[
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
16 Creates a 2-column cross reference between a list of input chains and all interacting chains found in the provided PDB database. This reference is required as
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
17 input for the SPRING min-Z calculator.
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
18 ]]></help>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
19 <tests>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
20 <test>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
21 <param name="list" value="cross/chains.tabular" />
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
22 <param name="index" value="cross/pdb.ffindex" />
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
23 <param name="database" value="cross/pdb.ffdata" />
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
24 <output name="output" file="cross/reference.tabular"/>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
25 </test>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
26 </tests>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
27 <citations>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
28 <citation type="bibtex">
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
29 @misc{githubhh-suite,
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
30 author = {Guerler, Govindarajoo, Zhang},
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
31 year = {2013},
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
32 title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction},
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
33 publisher = {ACS Publications},
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
34 journal = {Journal of Chemical Information and Modeling},
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
35 url = {https://pubs.acs.org/doi/10.1021/ci300579r},
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
36 }
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
37 </citation>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
38 </citations>
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
guerler
parents:
diff changeset
39 </tool>