Mercurial > repos > guerler > springsuite
annotate spring_minz.xml @ 31:3071750405c9 draft
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author | guerler |
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date | Tue, 24 Nov 2020 17:12:07 +0000 |
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1 <tool id="spring_minz" name="SPRING min-Z" version="0.1.2" python_template_version="3.5" license="MIT"> |
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2 <description>filter operation</description> |
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3 <command detect_errors="exit_code"><![CDATA[ |
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4 mkdir -p targets && |
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5 #for target in $targets |
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6 link '${str(target)}' 'targets/${target.element_identifier}' && |
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7 echo '${target.element_identifier}' >> 'target_list' && |
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8 #end for |
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9 #if str($input_type.input_type_selector) == "true": |
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10 mkdir -p inputs && |
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11 #for input in $input_type.inputs |
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12 link '${str(input)}' 'inputs/${input.element_identifier}' && |
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13 echo '${input.element_identifier}' >> 'input_list' && |
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14 #end for |
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15 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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16 #else |
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17 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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18 #end if |
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19 ]]></command> |
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20 <inputs> |
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21 <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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22 <conditional name="input_type"> |
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23 <param name="input_type_selector" type="boolean" label="Identify interactions across sets?" checked="true"/> |
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24 <when value="true"> |
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25 <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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26 </when> |
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27 </conditional> |
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28 <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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29 <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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30 <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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31 </inputs> |
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32 <outputs> |
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33 <data format="tabular" name="output" label="SPRING min-Z Table"/> |
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34 <data format="txt" name="log" label="SPRING min-Z Log" /> |
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35 </outputs> |
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36 <tests> |
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37 <test> |
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38 <param name="targets"> |
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39 <collection type="list"> |
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40 <element name="7BQY_A.hhr" value="minz/7BQY_A.hhr" /> |
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41 <element name="6WLC_A.hhr" value="minz/6WLC_A.hhr" /> |
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42 <element name="6WJI_A.hhr" value="minz/6WJI_A.hhr" /> |
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43 <element name="6WEY_A.hhr" value="minz/6WEY_A.hhr" /> |
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44 <element name="6W37_A.hhr" value="minz/6W37_A.hhr" /> |
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45 <element name="6W9C_A.hhr" value="minz/6W9C_A.hhr" /> |
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46 <element name="6W4H_B.hhr" value="minz/6W4H_B.hhr" /> |
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47 <element name="6W4H_A.hhr" value="minz/6W4H_A.hhr" /> |
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48 <element name="6W9Q_A.hhr" value="minz/6W9Q_A.hhr" /> |
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49 </collection> |
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50 </param> |
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51 <conditional name="input_type"> |
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52 <param name="input_type_selector" type="boolean" checked="false"/> |
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53 </conditional> |
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54 <param name="crossreference" value="minz/dbCAN_random.txt"/> |
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55 <param name="idx" type="integer" value="10"/> |
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56 <output name="output" file="minz/dbCAN_result.txt"/> |
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57 <output name="log" file="minz/dbCAN_log.txt"/> |
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58 </test> |
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59 <test> |
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60 <param name="targets"> |
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61 <collection type="list"> |
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62 <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" /> |
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63 </collection> |
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64 </param> |
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65 <conditional name="input_type"> |
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66 <param name="input_type_selector" type="boolean" checked="true"/> |
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67 <param name="inputs"> |
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68 <collection type="list"> |
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69 <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" /> |
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70 <element name="NP_000290.2.hhr" value="minz/NP_000290.2.hhr" /> |
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71 <element name="NP_000548.2.hhr" value="minz/NP_000548.2.hhr" /> |
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72 <element name="NP_000836.2.hhr" value="minz/NP_000836.2.hhr" /> |
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73 </collection> |
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74 </param> |
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75 </conditional> |
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76 <param name="crossreference" value="minz/pdb70_random.txt"/> |
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77 <output name="output" file="minz/pdb70_result.txt"/> |
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78 <output name="log" file="minz/pdb70_log.txt"/> |
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79 </test> |
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80 </tests> |
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81 <help><![CDATA[ |
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82 This tool filters HH-search/HH-blits homology results through the protein interaction cross reference generated by SPRING. |
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83 Putative interactions are identified by evaluating the min-Z score. |
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84 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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85 ]]></help> |
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86 <citations> |
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87 <citation type="bibtex"> |
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88 @misc{githubhh-suite, |
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89 author = {Guerler, Govindarajoo, Zhang}, |
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90 year = {2013}, |
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91 title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction}, |
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92 publisher = {ACS Publications}, |
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93 journal = {Journal of Chemical Information and Modeling}, |
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94 url = {https://pubs.acs.org/doi/10.1021/ci300579r}, |
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95 } |
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96 </citation> |
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97 </citations> |
d30785e31577
"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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98 </tool> |