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comparison 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
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children b2d4238b09d1
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-1:000000000000 0:0fdd5f2a7a53
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>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p targets &&
9 #for target in $targets
10 ln -s '${target}' 'targets/${target.element_identifier}' &&
11 echo '${target.element_identifier}' >> 'target_list' &&
12 #end for
13 #if $input_type.input_type_selector == "yes":
14 mkdir -p ./inputs &&
15 #for input in $input_type.inputs
16 ln -s '${input}' 'inputs/${input.element_identifier}' &&
17 echo '${input.element_identifier}' >> 'input_list' &&
18 #end for
19 spring_minz.py
20 -tl target_list
21 -tp targets
22 -il input_list
23 -ip inputs
24 -m '$minscore'
25 -c '$crossreference'
26 -o '$output'
27 -l '$log'
28 #else
29 spring_minz.py
30 -tl target_list
31 -tp targets
32 -m '$minscore'
33 -c '$crossreference'
34 -o '$output'
35 -l '$log'
36 #end if
37 ]]> </command>
38 <inputs>
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">
41 <param name="input_type_selector" type="select" label="Identify interactions across sets?">
42 <option value="yes" selected="True">yes</option>
43 <option value="no">no</option>
44 </param>
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."/>
47 </when>
48 <when value="no"/>
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`."/>
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"/>
53 </inputs>
54 <outputs>
55 <data format="tabular" name="output" label="SPRING min-Z Table"/>
56 <data format="txt" name="log" label="SPRING min-Z Log">
57 <filter>logfile</filter>
58 </data>
59 </outputs>
60 <tests>
61 <test expect_num_outputs="1">
62 <param name="targets">
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">
71 <param name="input_type_selector" value="false"/>
72 </conditional>
73 <param name="crossreference" value="minz/pdb70_random.txt"/>
74 <output name="output" file="minz/pdb70_result.0.txt"/>
75 </test>
76 <test expect_num_outputs="1">
77 <param name="targets">
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">
83 <param name="input_type_selector" value="true"/>
84 <param name="inputs">
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>
93 <param name="crossreference" value="minz/pdb70_random.txt"/>
94 <output name="output" file="minz/pdb70_result.1.txt"/>
95 </test>
96 </tests>
97 <help><![CDATA[
98
99 **What it does**
100
101 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.
103 The min-Z is the smaller of the two Z-scores for a pair of sequences matching an existing protein-protein complex structure.
104
105 ]]> </help>
106 <expand macro="citations"/>
107 </tool>