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comparison spring_minz.xml @ 39:172398348efd draft

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"planemo upload commit 26b4018c88041ee0ca7c2976e0a012015173d7b6-dirty"
author guerler
date Fri, 22 Jan 2021 15:50:27 +0000
parents 0be0af9e695d
children
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38:80a4b98121b6 39:172398348efd
10 mkdir -p inputs && 10 mkdir -p inputs &&
11 #for input in $input_type.inputs 11 #for input in $input_type.inputs
12 link '${str(input)}' 'inputs/${input.element_identifier}' && 12 link '${str(input)}' 'inputs/${input.element_identifier}' &&
13 echo '${input.element_identifier}' >> 'input_list' && 13 echo '${input.element_identifier}' >> 'input_list' &&
14 #end for 14 #end for
15 python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -il input_list -ip inputs -m '$minscore' -idx '$idx' -c '$crossreference' -o '$output' -l '$log' 15 python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -il input_list -ip inputs -m '$minscore' -c '$crossreference' -o '$output' -l '$log'
16 #else 16 #else
17 python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -m '$minscore' -idx '$idx' -c '$crossreference' -o '$output' -l '$log' 17 python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -m '$minscore' -c '$crossreference' -o '$output' -l '$log'
18 #end if 18 #end if
19 ]]></command> 19 ]]></command>
20 <inputs> 20 <inputs>
21 <param format="txt" name="targets" type="data_collection" collection_type="list" label="Target profiles" help="Homology search result of target/query profiles `hhr`."/> 21 <param format="txt" name="targets" type="data_collection" collection_type="list" label="Target profiles" help="Homology search result of target/query profiles `hhr`."/>
22 <conditional name="input_type"> 22 <conditional name="input_type">
25 <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input profiles" help="Homology search results of input profiles `hhr`."/> 25 <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input profiles" help="Homology search results of input profiles `hhr`."/>
26 </when> 26 </when>
27 </conditional> 27 </conditional>
28 <param format="tabular" name="crossreference" type="data" label="Cross reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/> 28 <param format="tabular" name="crossreference" type="data" label="Cross reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/>
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."/> 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."/>
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."/>
31 </inputs> 30 </inputs>
32 <outputs> 31 <outputs>
33 <data format="tabular" name="output" label="SPRING min-Z Table"/> 32 <data format="tabular" name="output" label="SPRING min-Z Table"/>
34 <data format="txt" name="log" label="SPRING min-Z Log" /> 33 <data format="txt" name="log" label="SPRING min-Z Log" />
35 </outputs> 34 </outputs>
36 <tests> 35 <tests>
37 <test> 36 <test>
38 <param name="targets"> 37 <param name="targets">
39 <collection type="list"> 38 <collection type="list">
40 <element name="7BQY_A.hhr" value="minz/7BQY_A.hhr" /> 39 <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" />
41 <element name="6WLC_A.hhr" value="minz/6WLC_A.hhr" /> 40 <element name="NP_000290.2.hhr" value="minz/NP_000290.2.hhr" />
42 <element name="6WJI_A.hhr" value="minz/6WJI_A.hhr" /> 41 <element name="NP_000548.2.hhr" value="minz/NP_000548.2.hhr" />
43 <element name="6WEY_A.hhr" value="minz/6WEY_A.hhr" /> 42 <element name="NP_000836.2.hhr" value="minz/NP_000836.2.hhr" />
44 <element name="6W37_A.hhr" value="minz/6W37_A.hhr" />
45 <element name="6W9C_A.hhr" value="minz/6W9C_A.hhr" />
46 <element name="6W4H_B.hhr" value="minz/6W4H_B.hhr" />
47 <element name="6W4H_A.hhr" value="minz/6W4H_A.hhr" />
48 <element name="6W9Q_A.hhr" value="minz/6W9Q_A.hhr" />
49 </collection> 43 </collection>
50 </param> 44 </param>
51 <conditional name="input_type"> 45 <conditional name="input_type">
52 <param name="input_type_selector" type="boolean" checked="false"/> 46 <param name="input_type_selector" type="boolean" checked="false"/>
53 </conditional> 47 </conditional>
54 <param name="crossreference" value="minz/dbCAN_random.txt"/> 48 <param name="crossreference" value="minz/pdb70_random.txt"/>
55 <param name="idx" type="integer" value="10"/> 49 <output name="output" file="minz/pdb70_result.0.txt"/>
56 <output name="output" file="minz/dbCAN_result.txt"/>
57 <output name="log" file="minz/dbCAN_log.txt"/>
58 </test> 50 </test>
59 <test> 51 <test>
60 <param name="targets"> 52 <param name="targets">
61 <collection type="list"> 53 <collection type="list">
62 <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" /> 54 <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" />
72 <element name="NP_000836.2.hhr" value="minz/NP_000836.2.hhr" /> 64 <element name="NP_000836.2.hhr" value="minz/NP_000836.2.hhr" />
73 </collection> 65 </collection>
74 </param> 66 </param>
75 </conditional> 67 </conditional>
76 <param name="crossreference" value="minz/pdb70_random.txt"/> 68 <param name="crossreference" value="minz/pdb70_random.txt"/>
77 <output name="output" file="minz/pdb70_result.txt"/> 69 <output name="output" file="minz/pdb70_result.1.txt"/>
78 <output name="log" file="minz/pdb70_log.txt"/>
79 </test> 70 </test>
80 </tests> 71 </tests>
81 <help><![CDATA[ 72 <help><![CDATA[
82 This tool filters HH-search/HH-blits homology results through the protein interaction cross reference generated by SPRING. 73 This tool filters HH-search/HH-blits homology results through the protein interaction cross reference generated by SPRING.
83 Putative interactions are identified by evaluating the min-Z score. 74 Putative interactions are identified by evaluating the min-Z score.