annotate spring_minz.xml @ 13:f8ba4dd48cbd draft

"planemo upload commit 6aa4b0a91f36999fab860591a4e33cdd6dcb70cf"
author guerler
date Sat, 26 Sep 2020 14:30:43 +0000
parents 0ea00dce62ab
children b53a98b90354
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
13
f8ba4dd48cbd "planemo upload commit 6aa4b0a91f36999fab860591a4e33cdd6dcb70cf"
guerler
parents: 12
diff changeset
1 <tool id="spring_minz" name="SPRING min-Z" version="0.1.1" python_template_version="3.5">
5
e44b8a76d754 "planemo upload commit 0f78008658d469b8c412a393050ac4ed9230b9ee-dirty"
guerler
parents: 4
diff changeset
2 <description>filter operation</description>
0
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
3 <code file="spring_minz.py"/>
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
4 <command detect_errors="exit_code"><![CDATA[
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
5 mkdir -p inputs &&
2
cc21dac19d25 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1-dirty"
guerler
parents: 0
diff changeset
6 #for input in $inputs
4
bde9a1a44a36 "planemo upload commit 3002402473e9f6dcdac5bfb4013cd2d81884a938"
guerler
parents: 3
diff changeset
7 link '${str(input)}' 'inputs/${input.element_identifier}' &&
bde9a1a44a36 "planemo upload commit 3002402473e9f6dcdac5bfb4013cd2d81884a938"
guerler
parents: 3
diff changeset
8 echo '${input.element_identifier}' >> 'input_list' &&
2
cc21dac19d25 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1-dirty"
guerler
parents: 0
diff changeset
9 #end for
11
21a7dd67b483 "planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
guerler
parents: 10
diff changeset
10 #for target in $targets
12
0ea00dce62ab "planemo upload commit 373d73ef3a09902e75f10084e30b271d84a6d7b1"
guerler
parents: 11
diff changeset
11 python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '${str(target)}' -n '${target.element_identifier}' -c '$crossreference' -x '$idx' -o '$output' -l input_list -i inputs &&
11
21a7dd67b483 "planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
guerler
parents: 10
diff changeset
12 #end for
12
0ea00dce62ab "planemo upload commit 373d73ef3a09902e75f10084e30b271d84a6d7b1"
guerler
parents: 11
diff changeset
13 echo 0
0
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
14 ]]></command>
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
15 <inputs>
11
21a7dd67b483 "planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
guerler
parents: 10
diff changeset
16 <param format="txt" name="targets" type="data_collection" label="Target Profiles" help="Homology search result of target/query profiles `hhr`."/>
7
2b9ed61195e2 "planemo upload commit ab5e686c62d07a0d45216b474d435b855745222d-dirty"
guerler
parents: 6
diff changeset
17 <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of input profiles `hhr`."/>
9
4ac5d5a9b21c "planemo upload commit f465445ebca0307953f59938494a2244ca8ea23c"
guerler
parents: 7
diff changeset
18 <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/>
7
2b9ed61195e2 "planemo upload commit ab5e686c62d07a0d45216b474d435b855745222d-dirty"
guerler
parents: 6
diff changeset
19 <param name="minscore" type="integer" label="min-Z score threshold" value="10" min="1" max="100" help="Matching interaction pairs with a score lower than this threshold will be excluded."/>
10
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
20 <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."/>
0
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
21 </inputs>
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
22 <outputs>
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
23 <data format="txt" name="output" />
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
24 </outputs>
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
25 <tests>
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
26 <test>
11
21a7dd67b483 "planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
guerler
parents: 10
diff changeset
27 <param name="targets">
21a7dd67b483 "planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
guerler
parents: 10
diff changeset
28 <collection type="list">
12
0ea00dce62ab "planemo upload commit 373d73ef3a09902e75f10084e30b271d84a6d7b1"
guerler
parents: 11
diff changeset
29 <element name="6W4H_A.hhr" value="6W4H_A.hhr" />
0ea00dce62ab "planemo upload commit 373d73ef3a09902e75f10084e30b271d84a6d7b1"
guerler
parents: 11
diff changeset
30 <element name="6W4H_B.hhr" value="6W4H_B.hhr" />
0ea00dce62ab "planemo upload commit 373d73ef3a09902e75f10084e30b271d84a6d7b1"
guerler
parents: 11
diff changeset
31 <element name="6W9C_A.hhr" value="6W9C_A.hhr" />
0ea00dce62ab "planemo upload commit 373d73ef3a09902e75f10084e30b271d84a6d7b1"
guerler
parents: 11
diff changeset
32 <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" />
0ea00dce62ab "planemo upload commit 373d73ef3a09902e75f10084e30b271d84a6d7b1"
guerler
parents: 11
diff changeset
33 <element name="6W37_A.hhr" value="6W37_A.hhr" />
0ea00dce62ab "planemo upload commit 373d73ef3a09902e75f10084e30b271d84a6d7b1"
guerler
parents: 11
diff changeset
34 <element name="6WEY_A.hhr" value="6WEY_A.hhr" />
0ea00dce62ab "planemo upload commit 373d73ef3a09902e75f10084e30b271d84a6d7b1"
guerler
parents: 11
diff changeset
35 <element name="6WJI_A.hhr" value="6WJI_A.hhr" />
0ea00dce62ab "planemo upload commit 373d73ef3a09902e75f10084e30b271d84a6d7b1"
guerler
parents: 11
diff changeset
36 <element name="6WLC_A.hhr" value="6WLC_A.hhr" />
11
21a7dd67b483 "planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
guerler
parents: 10
diff changeset
37 <element name="7BQY_A.hhr" value="7BQY_A.hhr" />
21a7dd67b483 "planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
guerler
parents: 10
diff changeset
38 </collection>
21a7dd67b483 "planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
guerler
parents: 10
diff changeset
39 </param>
10
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
40 <param name="idx" value="10"/>
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
41 <param name="inputs">
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
42 <collection type="list">
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
43 <element name="6W4H_A.hhr" value="6W4H_A.hhr" />
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
44 <element name="6W4H_B.hhr" value="6W4H_B.hhr" />
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
45 <element name="6W9C_A.hhr" value="6W9C_A.hhr" />
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
46 <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" />
12
0ea00dce62ab "planemo upload commit 373d73ef3a09902e75f10084e30b271d84a6d7b1"
guerler
parents: 11
diff changeset
47 <element name="6W37_A.hhr" value="6W37_A.hhr" />
10
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
48 <element name="6WEY_A.hhr" value="6WEY_A.hhr" />
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
49 <element name="6WJI_A.hhr" value="6WJI_A.hhr" />
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
50 <element name="6WLC_A.hhr" value="6WLC_A.hhr" />
12
0ea00dce62ab "planemo upload commit 373d73ef3a09902e75f10084e30b271d84a6d7b1"
guerler
parents: 11
diff changeset
51 <element name="7BQY_A.hhr" value="7BQY_A.hhr" />
10
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
52 </collection>
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
53 </param>
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
54 <param name="crossreference" value="dbCAN_random.txt"/>
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
55 <output name="output" file="dbCAN_result.txt"/>
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
56 </test>
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
57 <test>
11
21a7dd67b483 "planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
guerler
parents: 10
diff changeset
58 <param name="targets">
21a7dd67b483 "planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
guerler
parents: 10
diff changeset
59 <collection type="list">
21a7dd67b483 "planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
guerler
parents: 10
diff changeset
60 <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
21a7dd67b483 "planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
guerler
parents: 10
diff changeset
61 </collection>
21a7dd67b483 "planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
guerler
parents: 10
diff changeset
62 </param>
0
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
63 <param name="inputs">
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
64 <collection type="list">
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
65 <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
66 <element name="NP_000290.2.hhr" value="NP_000290.2.hhr" />
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
67 <element name="NP_000548.2.hhr" value="NP_000548.2.hhr" />
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
68 <element name="NP_000836.2.hhr" value="NP_000836.2.hhr" />
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
69 </collection>
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
70 </param>
10
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
71 <param name="crossreference" value="pdb70_random.txt"/>
860bd6f8f480 "planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
guerler
parents: 9
diff changeset
72 <output name="output" file="pdb70_result.txt"/>
0
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
73 </test>
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
74 </tests>
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
75 <help><![CDATA[
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
76 This tool filters HH-search/HH-blits homology results through the protein interaction cross reference generated by SPRING. Putative interactions are identified by
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
77 evaluating the min-Z score. The min-Z is the smaller of the two Z-scores for a pair of sequences matching an existing protein-protein complex structure.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
78 ]]></help>
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
79 <citations>
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
80 <citation type="bibtex">
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
81 @misc{githubhh-suite,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
82 author = {Guerler, Govindarajoo, Zhang},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
83 year = {2013},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
84 title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
85 publisher = {ACS Publications},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
86 journal = {Journal of Chemical Information and Modeling},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
87 url = {https://pubs.acs.org/doi/10.1021/ci300579r},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
88 }
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
89 </citation>
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
90 </citations>
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
91 </tool>