annotate spring_minz.xml @ 28:75d1aedc9b3f draft

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author guerler
date Sat, 31 Oct 2020 22:55:35 +0000
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1 <tool id="spring_minz" name="SPRING min-Z" version="0.1.2" 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 targets &&
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6 #for target in $targets
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7 link '${str(target)}' 'targets/${target.element_identifier}' &&
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8 echo '${target.element_identifier}' >> 'target_list' &&
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9 #end for
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10 #if str($input_type.input_type_selector) == "true":
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11 mkdir -p inputs &&
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12 #for input in $input_type.inputs
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13 link '${str(input)}' 'inputs/${input.element_identifier}' &&
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14 echo '${input.element_identifier}' >> 'input_list' &&
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15 #end for
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16 python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -il input_list -ip inputs -m '$minscore' -idx '$idx' -c '$crossreference' -o '$output' -l '$log'
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17 #else
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18 python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -m '$minscore' -idx '$idx' -c '$crossreference' -o '$output' -l '$log'
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19 #end if
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20 ]]></command>
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21 <inputs>
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22 <param format="txt" name="targets" type="data_collection" collection_type="list" label="Target profiles" help="Homology search result of target/query profiles `hhr`."/>
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23 <conditional name="input_type">
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24 <param name="input_type_selector" type="boolean" label="Identify interactions across sets?" checked="true"/>
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25 <when value="true">
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26 <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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27 </when>
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28 </conditional>
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29 <param format="tabular" name="crossreference" type="data" label="Cross reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/>
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30 <param name="minscore" type="integer" label="Score threshold" value="10" min="1" max="200" help="Matching interaction pairs with a score lower than this threshold will be excluded."/>
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31 <param name="idx" type="integer" label="Identifier length" value="6" min="1" max="20" help="Specify the length of the identifier e.g. `1ACB_A` has length 6."/>
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32 </inputs>
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33 <outputs>
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34 <data format="tabular" name="output" label="SPRING min-Z Table"/>
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35 <data format="txt" name="log" label="SPRING min-Z Log" />
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="targets">
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40 <collection type="list">
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41 <element name="7BQY_A.hhr" value="minz/7BQY_A.hhr" />
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42 <element name="6WLC_A.hhr" value="minz/6WLC_A.hhr" />
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43 <element name="6WJI_A.hhr" value="minz/6WJI_A.hhr" />
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44 <element name="6WEY_A.hhr" value="minz/6WEY_A.hhr" />
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45 <element name="6W37_A.hhr" value="minz/6W37_A.hhr" />
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46 <element name="6W9C_A.hhr" value="minz/6W9C_A.hhr" />
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47 <element name="6W4H_B.hhr" value="minz/6W4H_B.hhr" />
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48 <element name="6W4H_A.hhr" value="minz/6W4H_A.hhr" />
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49 <element name="6W9Q_A.hhr" value="minz/6W9Q_A.hhr" />
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50 </collection>
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51 </param>
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52 <conditional name="input_type">
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53 <param name="input_type_selector" type="boolean" checked="false"/>
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54 </conditional>
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55 <param name="crossreference" value="minz/dbCAN_random.txt"/>
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56 <param name="idx" type="integer" value="10"/>
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57 <output name="output" file="minz/dbCAN_result.txt"/>
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58 <output name="log" file="minz/dbCAN_log.txt"/>
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59 </test>
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60 <test>
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61 <param name="targets">
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62 <collection type="list">
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63 <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" />
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64 </collection>
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65 </param>
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66 <conditional name="input_type">
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67 <param name="input_type_selector" type="boolean" checked="true"/>
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68 <param name="inputs">
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69 <collection type="list">
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70 <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" />
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71 <element name="NP_000290.2.hhr" value="minz/NP_000290.2.hhr" />
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72 <element name="NP_000548.2.hhr" value="minz/NP_000548.2.hhr" />
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73 <element name="NP_000836.2.hhr" value="minz/NP_000836.2.hhr" />
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74 </collection>
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75 </param>
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76 </conditional>
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77 <param name="crossreference" value="minz/pdb70_random.txt"/>
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78 <output name="output" file="minz/pdb70_result.txt"/>
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79 <output name="log" file="minz/pdb70_log.txt"/>
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80 </test>
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81 </tests>
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82 <help><![CDATA[
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83 This tool filters HH-search/HH-blits homology results through the protein interaction cross reference generated by SPRING.
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84 Putative interactions are identified by evaluating the min-Z score.
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85 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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86 ]]></help>
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87 <citations>
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88 <citation type="bibtex">
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89 @misc{githubhh-suite,
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90 author = {Guerler, Govindarajoo, Zhang},
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91 year = {2013},
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92 title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction},
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93 publisher = {ACS Publications},
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94 journal = {Journal of Chemical Information and Modeling},
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95 url = {https://pubs.acs.org/doi/10.1021/ci300579r},
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96 }
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97 </citation>
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98 </citations>
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99 </tool>