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annotate spring_minz.xml @ 2:cc21dac19d25 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1-dirty"
author guerler
date Fri, 31 Jul 2020 01:49:36 -0400
parents d30785e31577
children c4b2e16845ab
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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 &&
2
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6 #for input in $inputs
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7 #try
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8 ln -s '${str(input)}' 'inputs/${input.name}' &&
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9 echo '${input.name}' >> 'input_list' &&
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10 #except
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11 #pass
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12 #end try
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13 #end for
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14 python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '$target' -c '$crossreference' -o '$output' -l input_list -i inputs
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15 ]]></command>
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16 <inputs>
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17 <param format="data" name="target" type="data" label="Target Sequence" help="Homology search results of query sequence `hhr`. (-t)"/>
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18 <param format="data" name="inputs" type="data_collection" collection_type="list" label="Input Sequences" help="Homology search results of target sequences `hhr`. (-i)"/>
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19 <param format="data" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins pairs. (-c)"/>
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20 <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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21 </inputs>
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22 <outputs>
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23 <data format="txt" name="output" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="target" value="NP_000282.1.hhr"/>
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28 <param name="inputs">
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29 <collection type="list">
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30 <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
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31 <element name="NP_000290.2.hhr" value="NP_000290.2.hhr" />
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32 <element name="NP_000548.2.hhr" value="NP_000548.2.hhr" />
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33 <element name="NP_000836.2.hhr" value="NP_000836.2.hhr" />
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34 </collection>
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35 </param>
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36 <param name="crossreference" value="index.txt"/>
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37 <output name="output" file="result.txt"/>
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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41 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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42 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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43 ]]></help>
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44 <citations>
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45 <citation type="bibtex">
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46 @misc{githubhh-suite,
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47 author = {Guerler, Govindarajoo, Zhang},
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48 year = {2013},
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49 title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction},
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50 publisher = {ACS Publications},
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51 journal = {Journal of Chemical Information and Modeling},
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52 url = {https://pubs.acs.org/doi/10.1021/ci300579r},
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53 }
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54 </citation>
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55 </citations>
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56 </tool>