Mercurial > repos > guerler > spring_minz

annotate spring_minz.xml @ 4:aaf729ca617f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
author guerler
date Thu, 08 Apr 2021 18:24:11 +0000
parents 576c88c2ed11
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
1 <tool id="spring_minz" name="SPRING Min-Z" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
2 <description>filter operation</description>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
3 <macros>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
4 <import>macros.xml</import>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
5 </macros>
1
b2d4238b09d1 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
6 <expand macro="requirements" />
0
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
8 mkdir -p targets &&
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
9 #for target in $targets
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
10 ln -s '${target}' 'targets/${target.element_identifier}' &&
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
11 echo '${target.element_identifier}' >> 'target_list' &&
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
12 #end for
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
13 #if $input_type.input_type_selector == "yes":
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
14 mkdir -p ./inputs &&
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
15 #for input in $input_type.inputs
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
16 ln -s '${input}' 'inputs/${input.element_identifier}' &&
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
17 echo '${input.element_identifier}' >> 'input_list' &&
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
18 #end for
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
19 spring_minz.py
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
20 -tl target_list
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
21 -tp targets
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
22 -il input_list
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
23 -ip inputs
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
24 -m '$minscore'
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
25 -c '$crossreference'
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
26 -o '$output'
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
27 -l '$log'
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
28 #else
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
29 spring_minz.py
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
30 -tl target_list
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
31 -tp targets
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
32 -m '$minscore'
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
33 -c '$crossreference'
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
34 -o '$output'
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
35 -l '$log'
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
36 #end if
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
37 ]]> </command>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
38 <inputs>
3
576c88c2ed11 "planemo upload commit 3e145bda7677bf7850a7aa6d0cc41413902d44c0"
guerler
parents: 2
diff changeset
39 <param name="targets" type="data" format="hhr" multiple="true" label="Target profiles" help="Homology search result of target/query profiles in 'hhr' format." />
0
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
40 <conditional name="input_type">
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
41 <param name="input_type_selector" type="select" label="Identify interactions across sets?">
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
42 <option value="yes" selected="True">yes</option>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
43 <option value="no">no</option>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
44 </param>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
45 <when value="yes">
3
576c88c2ed11 "planemo upload commit 3e145bda7677bf7850a7aa6d0cc41413902d44c0"
guerler
parents: 2
diff changeset
46 <param name="inputs" format="hhr" type="data" multiple="true" label="Input profiles" help="Homology search results of input profiles in 'hhr' format." />
0
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
47 </when>
1
b2d4238b09d1 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
48 <when value="no" />
0
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
49 </conditional>
2
e311ac3ce995 "planemo upload commit e3e80ffb20dc853056edb611668861d0a154f3eb"
guerler
parents: 1
diff changeset
50 <param name="crossreference" format="tabular" type="data" label="Cross reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/>
e311ac3ce995 "planemo upload commit e3e80ffb20dc853056edb611668861d0a154f3eb"
guerler
parents: 1
diff changeset
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."/>
1
b2d4238b09d1 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
52 <expand macro="logfile" />
0
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
53 </inputs>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
54 <outputs>
1
b2d4238b09d1 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
55 <data format="tabular" name="output" label="SPRING min-Z Table" />
0
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
56 <data format="txt" name="log" label="SPRING min-Z Log">
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
57 <filter>logfile</filter>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
58 </data>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
59 </outputs>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
60 <tests>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
61 <test expect_num_outputs="1">
3
576c88c2ed11 "planemo upload commit 3e145bda7677bf7850a7aa6d0cc41413902d44c0"
guerler
parents: 2
diff changeset
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" />
0
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
63 <conditional name="input_type">
1
b2d4238b09d1 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
64 <param name="input_type_selector" value="no" />
0
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
65 </conditional>
1
b2d4238b09d1 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
66 <param name="crossreference" value="minz/pdb70_random.txt" />
b2d4238b09d1 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
67 <output name="output" file="minz/pdb70_result.0.txt" />
0
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
68 </test>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
69 <test expect_num_outputs="1">
3
576c88c2ed11 "planemo upload commit 3e145bda7677bf7850a7aa6d0cc41413902d44c0"
guerler
parents: 2
diff changeset
70 <param name="targets" value="minz/NP_000282.1.hhr" ftype="hhr" />
0
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
71 <conditional name="input_type">
1
b2d4238b09d1 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
72 <param name="input_type_selector" value="yes" />
3
576c88c2ed11 "planemo upload commit 3e145bda7677bf7850a7aa6d0cc41413902d44c0"
guerler
parents: 2
diff changeset
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" />
0
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
74 </conditional>
1
b2d4238b09d1 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
75 <param name="crossreference" value="minz/pdb70_random.txt" />
b2d4238b09d1 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
76 <output name="output" file="minz/pdb70_result.1.txt" />
0
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
77 </test>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
78 </tests>
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
79 <help><![CDATA[
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
80
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
81 **What it does**
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
82
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
83 This tool filters HH-search/HH-blits homology results through the protein interaction cross reference generated by SPRING.
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
84 Putative interactions are identified by evaluating the min-Z score.
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
85 The min-Z is the smaller of the two Z-scores for a pair of sequences matching an existing protein-protein complex structure.
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
86
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
87 ]]> </help>
1
b2d4238b09d1 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
88 <expand macro="citations" />
0
0fdd5f2a7a53 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
89 </tool>