annotate spring_minz.xml @ 9:4ac5d5a9b21c draft

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author guerler
date Sat, 01 Aug 2020 02:13:31 -0400
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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' -x '$idx' -o '$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 result of target/query profile `hhr`."/>
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14 <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of input profiles `hhr`."/>
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15 <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/>
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16 <param name="minscore" type="integer" label="min-Z score threshold" value="10" min="1" max="100" help="Matching interaction pairs with a score lower than this threshold will be excluded."/>
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17 <param name="idx" type="integer" label="Identifier length" value="6" min="1" max="10" help="Specify the length of the identifier e.g. `1ACB_A` has length 6."/>
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18 </inputs>
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19 <outputs>
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20 <data format="txt" name="output" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="target" value="NP_000282.1.hhr"/>
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25 <param name="inputs">
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26 <collection type="list">
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27 <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
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28 <element name="NP_000290.2.hhr" value="NP_000290.2.hhr" />
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29 <element name="NP_000548.2.hhr" value="NP_000548.2.hhr" />
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30 <element name="NP_000836.2.hhr" value="NP_000836.2.hhr" />
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31 </collection>
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32 </param>
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33 <param name="crossreference" value="index.txt"/>
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34 <output name="output" file="result.txt"/>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 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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39 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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40 ]]></help>
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41 <citations>
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42 <citation type="bibtex">
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43 @misc{githubhh-suite,
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44 author = {Guerler, Govindarajoo, Zhang},
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45 year = {2013},
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46 title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction},
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47 publisher = {ACS Publications},
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48 journal = {Journal of Chemical Information and Modeling},
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49 url = {https://pubs.acs.org/doi/10.1021/ci300579r},
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50 }
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51 </citation>
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52 </citations>
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53 </tool>