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comparison spring_minz.xml @ 1:b2d4238b09d1 draft

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"planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
author guerler
date Mon, 29 Mar 2021 21:49:29 +0000
parents 0fdd5f2a7a53
children e311ac3ce995
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0:0fdd5f2a7a53 1:b2d4238b09d1
1 <tool id="spring_minz" name="SPRING Min-Z" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="spring_minz" name="SPRING Min-Z" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>filter operation</description> 2 <description>filter operation</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p targets && 8 mkdir -p targets &&
9 #for target in $targets 9 #for target in $targets
10 ln -s '${target}' 'targets/${target.element_identifier}' && 10 ln -s '${target}' 'targets/${target.element_identifier}' &&
11 echo '${target.element_identifier}' >> 'target_list' && 11 echo '${target.element_identifier}' >> 'target_list' &&
34 -o '$output' 34 -o '$output'
35 -l '$log' 35 -l '$log'
36 #end if 36 #end if
37 ]]> </command> 37 ]]> </command>
38 <inputs> 38 <inputs>
39 <param name="targets" format="hhr" multiple="true" label="Target profiles" help="Homology search result of target/query profiles in 'hhr' format."/> 39 <param name="targets" format="hhr" multiple="true" label="Target profiles" help="Homology search result of target/query profiles in 'hhr' format." />
40 <conditional name="input_type"> 40 <conditional name="input_type">
41 <param name="input_type_selector" type="select" label="Identify interactions across sets?"> 41 <param name="input_type_selector" type="select" label="Identify interactions across sets?">
42 <option value="yes" selected="True">yes</option> 42 <option value="yes" selected="True">yes</option>
43 <option value="no">no</option> 43 <option value="no">no</option>
44 </param> 44 </param>
45 <when value="yes"> 45 <when value="yes">
46 <param name="inputs" format="hhr" multiple="true" label="Input profiles" help="Homology search results of input profiles in 'hhr' format."/> 46 <param name="inputs" format="hhr" multiple="true" label="Input profiles" help="Homology search results of input profiles in 'hhr' format." />
47 </when> 47 </when>
48 <when value="no"/> 48 <when value="no" />
49 </conditional> 49 </conditional>
50 <param name="crossreference" format="tabular" type="data" label="Cross reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/> 50 <param name="crossreference" format="tabular" type="data" label="Cross reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`." />
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."/> 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." />
52 <expand macro="logfile"/> 52 <expand macro="logfile" />
53 </inputs> 53 </inputs>
54 <outputs> 54 <outputs>
55 <data format="tabular" name="output" label="SPRING min-Z Table"/> 55 <data format="tabular" name="output" label="SPRING min-Z Table" />
56 <data format="txt" name="log" label="SPRING min-Z Log"> 56 <data format="txt" name="log" label="SPRING min-Z Log">
57 <filter>logfile</filter> 57 <filter>logfile</filter>
58 </data> 58 </data>
59 </outputs> 59 </outputs>
60 <tests> 60 <tests>
61 <test expect_num_outputs="1"> 61 <test expect_num_outputs="1">
62 <param name="targets"> 62 <param name="targets" value="minz/NP_000282.1.hhr,minz/NP_000290.2.hhr,minz/NP_000548.2.hhr,minz/NP_000836.2.hhr" ftype="hhr" />
63 <collection type="list">
64 <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" ftype="hhr"/>
65 <element name="NP_000290.2.hhr" value="minz/NP_000290.2.hhr" ftype="hhr"/>
66 <element name="NP_000548.2.hhr" value="minz/NP_000548.2.hhr" ftype="hhr"/>
67 <element name="NP_000836.2.hhr" value="minz/NP_000836.2.hhr" ftype="hhr"/>
68 </collection>
69 </param>
70 <conditional name="input_type"> 63 <conditional name="input_type">
71 <param name="input_type_selector" value="false"/> 64 <param name="input_type_selector" value="no" />
72 </conditional> 65 </conditional>
73 <param name="crossreference" value="minz/pdb70_random.txt"/> 66 <param name="crossreference" value="minz/pdb70_random.txt" />
74 <output name="output" file="minz/pdb70_result.0.txt"/> 67 <output name="output" file="minz/pdb70_result.0.txt" />
75 </test> 68 </test>
76 <test expect_num_outputs="1"> 69 <test expect_num_outputs="1">
77 <param name="targets"> 70 <param name="targets" value="minz/NP_000282.1.hhr" ftype="hhr" />
78 <collection type="list">
79 <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" ftype="hhr"/>
80 </collection>
81 </param>
82 <conditional name="input_type"> 71 <conditional name="input_type">
83 <param name="input_type_selector" value="true"/> 72 <param name="input_type_selector" value="yes" />
84 <param name="inputs"> 73 <param name="inputs" value="minz/NP_000282.1.hhr,minz/NP_000290.2.hhr,minz/NP_000548.2.hhr,minz/NP_000836.2.hhr" ftype="hhr" />
85 <collection type="list">
86 <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" ftype="hhr"/>
87 <element name="NP_000290.2.hhr" value="minz/NP_000290.2.hhr" ftype="hhr"/>
88 <element name="NP_000548.2.hhr" value="minz/NP_000548.2.hhr" ftype="hhr"/>
89 <element name="NP_000836.2.hhr" value="minz/NP_000836.2.hhr" ftype="hhr"/>
90 </collection>
91 </param>
92 </conditional> 74 </conditional>
93 <param name="crossreference" value="minz/pdb70_random.txt"/> 75 <param name="crossreference" value="minz/pdb70_random.txt" />
94 <output name="output" file="minz/pdb70_result.1.txt"/> 76 <output name="output" file="minz/pdb70_result.1.txt" />
95 </test> 77 </test>
96 </tests> 78 </tests>
97 <help><![CDATA[ 79 <help><![CDATA[
98 80
99 **What it does** 81 **What it does**
101 This tool filters HH-search/HH-blits homology results through the protein interaction cross reference generated by SPRING. 83 This tool filters HH-search/HH-blits homology results through the protein interaction cross reference generated by SPRING.
102 Putative interactions are identified by evaluating the min-Z score. 84 Putative interactions are identified by evaluating the min-Z score.
103 The min-Z is the smaller of the two Z-scores for a pair of sequences matching an existing protein-protein complex structure. 85 The min-Z is the smaller of the two Z-scores for a pair of sequences matching an existing protein-protein complex structure.
104 86
105 ]]> </help> 87 ]]> </help>
106 <expand macro="citations"/> 88 <expand macro="citations" />
107 </tool> 89 </tool>