Mercurial > repos > guerler > spring_minz

annotate spring_minz.xml @ 0:0fdd5f2a7a53 draft

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"planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
author guerler
date Tue, 23 Mar 2021 13:56:20 +0000
parents
children b2d4238b09d1
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1 <tool id="spring_minz" name="SPRING Min-Z" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>filter operation</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 mkdir -p targets &&
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9 #for target in $targets
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10 ln -s '${target}' 'targets/${target.element_identifier}' &&
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11 echo '${target.element_identifier}' >> 'target_list' &&
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12 #end for
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13 #if $input_type.input_type_selector == "yes":
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14 mkdir -p ./inputs &&
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15 #for input in $input_type.inputs
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16 ln -s '${input}' 'inputs/${input.element_identifier}' &&
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17 echo '${input.element_identifier}' >> 'input_list' &&
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18 #end for
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19 spring_minz.py
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20 -tl target_list
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21 -tp targets
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22 -il input_list
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23 -ip inputs
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24 -m '$minscore'
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25 -c '$crossreference'
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26 -o '$output'
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27 -l '$log'
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28 #else
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29 spring_minz.py
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30 -tl target_list
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31 -tp targets
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32 -m '$minscore'
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33 -c '$crossreference'
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34 -o '$output'
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35 -l '$log'
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36 #end if
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37 ]]> </command>
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38 <inputs>
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39 <param name="targets" format="hhr" multiple="true" label="Target profiles" help="Homology search result of target/query profiles in 'hhr' format."/>
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40 <conditional name="input_type">
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41 <param name="input_type_selector" type="select" label="Identify interactions across sets?">
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42 <option value="yes" selected="True">yes</option>
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43 <option value="no">no</option>
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44 </param>
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45 <when value="yes">
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46 <param name="inputs" format="hhr" multiple="true" label="Input profiles" help="Homology search results of input profiles in 'hhr' format."/>
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47 </when>
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48 <when value="no"/>
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49 </conditional>
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50 <param name="crossreference" format="tabular" type="data" label="Cross reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/>
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51 <param name="minscore" type="integer" value="10" min="1" max="200" label="Score threshold" help="Matching interaction pairs with a score lower than this threshold will be excluded."/>
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52 <expand macro="logfile"/>
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53 </inputs>
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54 <outputs>
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55 <data format="tabular" name="output" label="SPRING min-Z Table"/>
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56 <data format="txt" name="log" label="SPRING min-Z Log">
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57 <filter>logfile</filter>
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58 </data>
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59 </outputs>
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60 <tests>
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61 <test expect_num_outputs="1">
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62 <param name="targets">
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63 <collection type="list">
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64 <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" ftype="hhr"/>
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65 <element name="NP_000290.2.hhr" value="minz/NP_000290.2.hhr" ftype="hhr"/>
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66 <element name="NP_000548.2.hhr" value="minz/NP_000548.2.hhr" ftype="hhr"/>
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67 <element name="NP_000836.2.hhr" value="minz/NP_000836.2.hhr" ftype="hhr"/>
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68 </collection>
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69 </param>
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70 <conditional name="input_type">
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71 <param name="input_type_selector" value="false"/>
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72 </conditional>
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73 <param name="crossreference" value="minz/pdb70_random.txt"/>
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74 <output name="output" file="minz/pdb70_result.0.txt"/>
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75 </test>
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76 <test expect_num_outputs="1">
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77 <param name="targets">
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78 <collection type="list">
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79 <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" ftype="hhr"/>
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80 </collection>
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81 </param>
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82 <conditional name="input_type">
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83 <param name="input_type_selector" value="true"/>
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84 <param name="inputs">
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85 <collection type="list">
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86 <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" ftype="hhr"/>
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87 <element name="NP_000290.2.hhr" value="minz/NP_000290.2.hhr" ftype="hhr"/>
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88 <element name="NP_000548.2.hhr" value="minz/NP_000548.2.hhr" ftype="hhr"/>
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89 <element name="NP_000836.2.hhr" value="minz/NP_000836.2.hhr" ftype="hhr"/>
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90 </collection>
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91 </param>
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92 </conditional>
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93 <param name="crossreference" value="minz/pdb70_random.txt"/>
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94 <output name="output" file="minz/pdb70_result.1.txt"/>
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95 </test>
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96 </tests>
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97 <help><![CDATA[
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98
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99 **What it does**
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100
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101 This tool filters HH-search/HH-blits homology results through the protein interaction cross reference generated by SPRING.
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102 Putative interactions are identified by evaluating the min-Z score.
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103 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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104
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105 ]]> </help>
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106 <expand macro="citations"/>
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107 </tool>