Mercurial > repos > guerler > springsuite
annotate spring_minz.xml @ 6:323f11769abf draft
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author | guerler |
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date | Fri, 31 Jul 2020 23:35:20 -0400 |
parents | e44b8a76d754 |
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1 <tool id="spring_minz" name="SPRING min-Z" version="0.1.0" python_template_version="3.5"> |
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2 <description>filter operation</description> |
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3 <code file="spring_minz.py"/> |
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4 <command detect_errors="exit_code"><![CDATA[ |
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5 mkdir -p inputs && |
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6 #for input in $inputs |
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7 link '${str(input)}' 'inputs/${input.element_identifier}' && |
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8 echo '${input.element_identifier}' >> 'input_list' && |
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9 #end for |
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10 python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '$target' -c '$crossreference' -o '$output' -l input_list -i inputs |
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11 ]]></command> |
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12 <inputs> |
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13 <param format="txt" name="target" type="data" label="Target Profile" help="Homology search results of query sequence `hhr`. (-t)"/> |
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14 <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of target sequences `hhr`. (-i)"/> |
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15 <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins pairs. (-c)"/> |
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16 <param name="minscore" type="integer" label="min-Z score threshold" value="10" min="1" max="100" help="Matching complex templates with a score lower than this threshold will be excluded. (-c)"/> |
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17 </inputs> |
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18 <outputs> |
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19 <data format="txt" name="output" /> |
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20 </outputs> |
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21 <tests> |
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22 <test> |
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23 <param name="target" value="NP_000282.1.hhr"/> |
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24 <param name="inputs"> |
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25 <collection type="list"> |
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26 <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" /> |
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27 <element name="NP_000290.2.hhr" value="NP_000290.2.hhr" /> |
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28 <element name="NP_000548.2.hhr" value="NP_000548.2.hhr" /> |
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29 <element name="NP_000836.2.hhr" value="NP_000836.2.hhr" /> |
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30 </collection> |
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31 </param> |
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32 <param name="crossreference" value="index.txt"/> |
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33 <output name="output" file="result.txt"/> |
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34 </test> |
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35 </tests> |
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36 <help><![CDATA[ |
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37 This tool filters HH-search/HH-blits homology results through the protein interaction cross reference generated by SPRING. Putative interactions are identified by |
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38 evaluating the min-Z score. The min-Z is the smaller of the two Z-scores for a pair of sequences matching an existing protein-protein complex structure. |
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39 ]]></help> |
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40 <citations> |
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41 <citation type="bibtex"> |
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42 @misc{githubhh-suite, |
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43 author = {Guerler, Govindarajoo, Zhang}, |
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44 year = {2013}, |
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45 title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction}, |
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46 publisher = {ACS Publications}, |
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47 journal = {Journal of Chemical Information and Modeling}, |
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48 url = {https://pubs.acs.org/doi/10.1021/ci300579r}, |
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49 } |
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50 </citation> |
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51 </citations> |
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52 </tool> |