annotate spring_minz.xml @ 19:dfd972ba93a4 draft

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author guerler
date Wed, 28 Oct 2020 05:15:42 +0000
parents c790d25086dc
children acaff61a09b2
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1 <tool id="spring_minz" name="SPRING min-Z" version="0.1.1" 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 mkdir -p targets &&
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11 #for target in $targets
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12 link '${str(target)}' 'targets/${target.element_identifier}' &&
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13 echo '${target.element_identifier}' >> 'target_list' &&
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14 #end for
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15 python3 '$__tool_directory__/spring_minz.py' -il input_list -ip inputs -tl target_list -tp targets -m '$minscore' -c '$crossreference' -x '$idx' -o '$output'
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16 ]]></command>
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17 <inputs>
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18 <param format="txt" name="targets" type="data_collection" label="Target Profiles" help="Homology search result of target/query profiles `hhr`."/>
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19 <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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20 <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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21 <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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22 <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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23 </inputs>
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24 <outputs>
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25 <data format="tabular" name="output" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="targets">
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30 <collection type="list">
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31 <element name="6W4H_A.hhr" value="6W4H_A.hhr" />
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32 <element name="6W4H_B.hhr" value="6W4H_B.hhr" />
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33 <element name="6W9C_A.hhr" value="6W9C_A.hhr" />
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34 <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" />
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35 <element name="6W37_A.hhr" value="6W37_A.hhr" />
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36 <element name="6WEY_A.hhr" value="6WEY_A.hhr" />
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37 <element name="6WJI_A.hhr" value="6WJI_A.hhr" />
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38 <element name="6WLC_A.hhr" value="6WLC_A.hhr" />
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39 <element name="7BQY_A.hhr" value="7BQY_A.hhr" />
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40 </collection>
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41 </param>
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42 <param name="idx" value="10"/>
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43 <param name="inputs">
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44 <collection type="list">
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45 <element name="6W4H_A.hhr" value="6W4H_A.hhr" />
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46 <element name="6W4H_B.hhr" value="6W4H_B.hhr" />
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47 <element name="6W9C_A.hhr" value="6W9C_A.hhr" />
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48 <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" />
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49 <element name="6W37_A.hhr" value="6W37_A.hhr" />
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50 <element name="6WEY_A.hhr" value="6WEY_A.hhr" />
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51 <element name="6WJI_A.hhr" value="6WJI_A.hhr" />
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52 <element name="6WLC_A.hhr" value="6WLC_A.hhr" />
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53 <element name="7BQY_A.hhr" value="7BQY_A.hhr" />
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54 </collection>
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55 </param>
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56 <param name="crossreference" value="dbCAN_random.txt"/>
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57 <output name="output" file="dbCAN_result.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="NP_000282.1.hhr" />
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63 </collection>
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64 </param>
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65 <param name="inputs">
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66 <collection type="list">
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67 <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
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68 <element name="NP_000290.2.hhr" value="NP_000290.2.hhr" />
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69 <element name="NP_000548.2.hhr" value="NP_000548.2.hhr" />
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70 <element name="NP_000836.2.hhr" value="NP_000836.2.hhr" />
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71 </collection>
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72 </param>
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73 <param name="crossreference" value="pdb70_random.txt"/>
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74 <output name="output" file="pdb70_result.txt"/>
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78 This tool creates 3D models from HH-search/HH-blits homology results utilized by SPRING.
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79 ]]></help>
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80 <citations>
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81 <citation type="bibtex">
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82 @misc{githubhh-suite,
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83 author = {Guerler, Govindarajoo, Zhang},
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84 year = {2013},
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85 title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction},
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86 publisher = {ACS Publications},
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87 journal = {Journal of Chemical Information and Modeling},
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88 url = {https://pubs.acs.org/doi/10.1021/ci300579r},
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89 }
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90 </citation>
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91 </citations>
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92 </tool>