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comparison spring_minz.xml @ 23:5469e19f1f96 draft

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"planemo upload commit 37a4c6844fd7ab1071ddf90f51915ec1a13c26b3"
author guerler
date Thu, 29 Oct 2020 13:04:47 +0000
parents acaff61a09b2
children 802daf2993b0
comparison
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22:acaff61a09b2 23:5469e19f1f96
1 <tool id="spring_minz" name="SPRING min-Z" version="0.1.1" python_template_version="3.5"> 1 <tool id="spring_minz" name="SPRING min-Z" version="0.1.1" python_template_version="3.5">
2 <description>filter operation</description> 2 <description>filter operation</description>
3 <code file="spring_minz.py"/> 3 <code file="spring_minz.py"/>
4 <command detect_errors="exit_code"><![CDATA[ 4 <command detect_errors="exit_code"><![CDATA[
5 mkdir -p inputs && 5 mkdir -p targets &&
6 #for input in $inputs
7 link '${str(input)}' 'inputs/${input.element_identifier}' &&
8 echo '${input.element_identifier}' >> 'input_list' &&
9 #end for
10 mkdir -p targets &&
11 #for target in $targets 6 #for target in $targets
12 link '${str(target)}' 'targets/${target.element_identifier}' && 7 link '${str(target)}' 'targets/${target.element_identifier}' &&
13 echo '${target.element_identifier}' >> 'target_list' && 8 echo '${target.element_identifier}' >> 'target_list' &&
14 #end for 9 #end for
15 python3 '$__tool_directory__/spring_minz.py' -il input_list -ip inputs -tl target_list -tp targets -m '$minscore' -c '$crossreference' -x '$idx' -o '$output' 10 #if str($input_type.input_type_selector) == "true":
11 mkdir -p inputs &&
12 #for input in $input_type.inputs
13 link '${str(input)}' 'inputs/${input.element_identifier}' &&
14 echo '${input.element_identifier}' >> 'input_list' &&
15 #end for
16 python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -il input_list -ip inputs -m '$minscore' -c '$crossreference' -x '$idx' -o '$output' -l '$log'
17 #else
18 python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -m '$minscore' -c '$crossreference' -x '$idx' -o '$output' -l '$log'
19 #end if
16 ]]></command> 20 ]]></command>
17 <inputs> 21 <inputs>
18 <param format="txt" name="targets" type="data_collection" label="Target Profiles" help="Homology search result of target/query profiles `hhr`."/> 22 <param format="txt" name="targets" type="data_collection" collection_type="list" label="Target Profiles" help="Homology search result of target/query profiles `hhr`."/>
19 <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of input profiles `hhr`."/> 23 <conditional name="input_type">
24 <param name="input_type_selector" type="boolean" label="Identify interactions across sets?" checked="true"/>
25 <when value="true">
26 <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of input profiles `hhr`."/>
27 </when>
28 </conditional>
20 <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/> 29 <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/>
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."/> 30 <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."/>
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."/> 31 <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."/>
23 </inputs> 32 </inputs>
24 <outputs> 33 <outputs>
25 <data format="tabular" name="output" /> 34 <data format="tabular" name="output" label="SPRING min-Z Table"/>
35 <data format="txt" name="log" label="SPRING min-Z Log" />
26 </outputs> 36 </outputs>
27 <tests> 37 <tests>
28 <test> 38 <test>
29 <param name="targets"> 39 <param name="targets">
30 <collection type="list"> 40 <collection type="list">
31 <element name="6WEY_A.hhr" value="6WEY_A.hhr" /> 41 <element name="7BQY_A.hhr" value="7BQY_A.hhr" />
42 <element name="6WLC_A.hhr" value="6WLC_A.hhr" />
32 <element name="6WJI_A.hhr" value="6WJI_A.hhr" /> 43 <element name="6WJI_A.hhr" value="6WJI_A.hhr" />
33 <element name="6WLC_A.hhr" value="6WLC_A.hhr" /> 44 <element name="6WEY_A.hhr" value="6WEY_A.hhr" />
34 <element name="7BQY_A.hhr" value="7BQY_A.hhr" />
35 <element name="6W37_A.hhr" value="6W37_A.hhr" /> 45 <element name="6W37_A.hhr" value="6W37_A.hhr" />
36 <element name="6W9C_A.hhr" value="6W9C_A.hhr" /> 46 <element name="6W9C_A.hhr" value="6W9C_A.hhr" />
47 <element name="6W4H_B.hhr" value="6W4H_B.hhr" />
37 <element name="6W4H_A.hhr" value="6W4H_A.hhr" /> 48 <element name="6W4H_A.hhr" value="6W4H_A.hhr" />
38 <element name="6W4H_B.hhr" value="6W4H_B.hhr" />
39 <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" /> 49 <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" />
40 </collection> 50 </collection>
41 </param> 51 </param>
52 <conditional name="input_type">
53 <param name="input_type_selector" type="boolean" checked="false"/>
54 </conditional>
42 <param name="idx" value="10"/> 55 <param name="idx" value="10"/>
43 <param name="inputs">
44 <collection type="list">
45 <element name="6WEY_A.hhr" value="6WEY_A.hhr" />
46 <element name="6WJI_A.hhr" value="6WJI_A.hhr" />
47 <element name="6WLC_A.hhr" value="6WLC_A.hhr" />
48 <element name="7BQY_A.hhr" value="7BQY_A.hhr" />
49 <element name="6W37_A.hhr" value="6W37_A.hhr" />
50 <element name="6W9C_A.hhr" value="6W9C_A.hhr" />
51 <element name="6W4H_A.hhr" value="6W4H_A.hhr" />
52 <element name="6W4H_B.hhr" value="6W4H_B.hhr" />
53 <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" />
54 </collection>
55 </param>
56 <param name="crossreference" value="dbCAN_random.txt"/> 56 <param name="crossreference" value="dbCAN_random.txt"/>
57 <output name="output" file="dbCAN_result.txt"/> 57 <output name="output" file="dbCAN_result.txt"/>
58 <output name="log" file="dbCAN_log.txt"/>
58 </test> 59 </test>
59 <test> 60 <test>
60 <param name="targets"> 61 <param name="targets">
61 <collection type="list"> 62 <collection type="list">
62 <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" /> 63 <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
63 </collection> 64 </collection>
64 </param> 65 </param>
65 <param name="inputs"> 66 <conditional name="input_type">
66 <collection type="list"> 67 <param name="input_type_selector" type="boolean" checked="true"/>
67 <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" /> 68 <param name="inputs">
68 <element name="NP_000290.2.hhr" value="NP_000290.2.hhr" /> 69 <collection type="list">
69 <element name="NP_000548.2.hhr" value="NP_000548.2.hhr" /> 70 <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
70 <element name="NP_000836.2.hhr" value="NP_000836.2.hhr" /> 71 <element name="NP_000290.2.hhr" value="NP_000290.2.hhr" />
71 </collection> 72 <element name="NP_000548.2.hhr" value="NP_000548.2.hhr" />
72 </param> 73 <element name="NP_000836.2.hhr" value="NP_000836.2.hhr" />
74 </collection>
75 </param>
76 </conditional>
73 <param name="crossreference" value="pdb70_random.txt"/> 77 <param name="crossreference" value="pdb70_random.txt"/>
74 <output name="output" file="pdb70_result.txt"/> 78 <output name="output" file="pdb70_result.txt"/>
79 <output name="log" file="pdb70_log.txt"/>
75 </test> 80 </test>
76 </tests> 81 </tests>
77 <help><![CDATA[ 82 <help><![CDATA[
78 This tool creates 3D models from HH-search/HH-blits homology results utilized by SPRING. 83 This tool creates 3D models from HH-search/HH-blits homology results utilized by SPRING.
79 ]]></help> 84 ]]></help>