Mercurial > repos > guerler > spring_cross

annotate spring_cross.xml @ 2:6c65d6ab20f5 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 18:14:13 +0000
parents efef4f6d3452
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
1 <tool id="spring_cross" name="SPRING Cross" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
2 <description>reference builder</description>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
3 <macros>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
4 <import>macros.xml</import>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
5 </macros>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
6 <expand macro="requirements" />
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
8 spring_cross.py
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
9 @pdb_source@
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
10 -o '$output'
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
11 -g '$log'
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
12 ]]></command>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
13 <inputs>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
14 <expand macro="pdb_source" />
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
15 <expand macro="logfile" />
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
16 </inputs>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
17 <outputs>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
18 <data format="tabular" name="output" label="SPRING Cross Reference" />
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
19 <data format="txt" name="log" label="SPRING Cross Log">
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
20 <filter>logfile</filter>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
21 </data>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
22 </outputs>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
23 <tests>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
24 <test expect_num_outputs="1">
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
25 <conditional name="pdb_source">
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
26 <param name="pdb_source_selector" value="history" />
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
27 <param name="ffindex" value="cross/pdb.ffindex" />
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
28 <param name="ffdata" value="cross/pdb.ffdata" />
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
29 </conditional>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
30 <param name="logfile" value="false" />
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
31 <output name="output" file="cross/reference.tabular" />
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
32 </test>
1
efef4f6d3452 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
33 <test expect_num_outputs="1">
efef4f6d3452 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
34 <conditional name="pdb_source">
efef4f6d3452 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
35 <param name="pdb_source_selector" value="indexed" />
efef4f6d3452 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
36 <param name="pdb" value="pdb02_cross" />
efef4f6d3452 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
37 <param name="zipped" value="gz" />
efef4f6d3452 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
38 </conditional>
efef4f6d3452 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
39 <param name="logfile" value="false" />
efef4f6d3452 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
40 <output name="output" file="cross/reference.tabular" />
efef4f6d3452 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
41 </test>
0
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
42 <test expect_num_outputs="2">
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
43 <conditional name="pdb_source">
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
44 <param name="pdb_source_selector" value="indexed" />
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
45 <param name="pdb" value="pdb01_cross" />
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
46 </conditional>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
47 <param name="logfile" value="true" />
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
48 <output name="output" file="cross/reference.tabular" />
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
49 </test>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
50 </tests>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
51 <help><![CDATA[
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
52
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
53 **What it does**
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
54
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
55 Creates a 2-column cross reference between a list of input chains and all interacting chains found in the provided PDB database.
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
56 This reference is required as input for the SPRING min-Z calculator.
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
57
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
58 ]]></help>
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
59 <expand macro="citations" />
282c58535ebc "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
60 </tool>