Mercurial > repos > guerler > ffindex_dbkit_create
comparison dbkit_create.xml @ 1:c1dff5c2a7b3 draft
"planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
author | guerler |
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date | Mon, 29 Mar 2021 21:45:54 +0000 |
parents | 8b48a608f1df |
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0:8b48a608f1df | 1:c1dff5c2a7b3 |
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1 <tool id="ffindex_dbkit_create" name="DBKit Create" version="0.1.1" license="MIT" profile="20.01"> | 1 <tool id="ffindex_dbkit_create" name="DBKit Create" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="20.01"> |
2 <description>database</description> | 2 <description>database</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
16 -d '$database' | 16 -d '$database' |
17 -g '$log' | 17 -g '$log' |
18 -il '$advanced.idlength' | 18 -il '$advanced.idlength' |
19 -ic '$advanced.idcase' | 19 -ic '$advanced.idcase' |
20 -ie '$advanced.idextension' | 20 -ie '$advanced.idextension' |
21 -ip '$advanced.idprefix' | |
21 ]]> </command> | 22 ]]> </command> |
22 <inputs> | 23 <inputs> |
23 <param name="input" type="data" format="tabular" label="List of Identifiers" help="Specify a list containing all entry identifiers to be downloaded." /> | 24 <param name="input" type="data" format="tabular" label="List of Identifiers" help="Specify a list containing all entry identifiers to be downloaded." /> |
24 <param name="inputs" type="data" format="txt" multiple="true" label="Specify your datasets" help="The datasets that you want to convert into an ffindex." /> | 25 <param name="inputs" type="data" format="txt" multiple="true" label="Specify your datasets" help="The datasets that you want to convert into an ffindex." /> |
25 <conditional name="advanced"> | 26 <conditional name="advanced"> |
26 <param name="type" type="select" label="Identifier Formatting Options" help=""> | 27 <param name="type" type="select" label="Identifier Formatting Options" help=""> |
27 <option value="true">Yes, I want to format my identifiers</option> | 28 <option value="true">Yes, I want to format my identifiers</option> |
28 <option value="false">No formatting</option> | 29 <option value="false">No formatting</option> |
29 </param> | 30 </param> |
30 <when value="true"> | 31 <when value="true"> |
31 <param name="idextension" type="text" optional="true" label="Identifier Extensions" help="Specify the extension of the identifier" /> | 32 <param name="idprefix" type="text" optional="true" label="Identifier Prefix" help="Specify the prefix of the identifier"> |
33 <validator type="regex" message="Please only use letters, numbers or underscores">^[a-zA-Z.]+$</validator> | |
34 </param> | |
35 <param name="idextension" type="text" optional="true" label="Identifier Extensions" help="Specify the extension of the identifier"> | |
36 <validator type="regex" message="Please only use letters, numbers or underscores">^[a-zA-Z.]+$</validator> | |
37 </param> | |
32 <param name="idlength" type="integer" label="Identifier Length" value="0" min="0" max="20" help="Specify the length of the identifier (disable=0)." /> | 38 <param name="idlength" type="integer" label="Identifier Length" value="0" min="0" max="20" help="Specify the length of the identifier (disable=0)." /> |
33 <param name="idcase" type="select" label="Identifier Case" display="radio" help="Choose to format the identifier by changing its case (optional)."> | 39 <param name="idcase" type="select" label="Identifier Case" display="radio" help="Choose to format the identifier by changing its case (optional)."> |
34 <option value="">Unformatted</option> | 40 <option value="">Unformatted</option> |
35 <option value="lower">Lower</option> | 41 <option value="lower">Lower</option> |
36 <option value="upper">Upper</option> | 42 <option value="upper">Upper</option> |
37 </param> | 43 </param> |
38 </when> | 44 </when> |
39 <when value="false"> | 45 <when value="false"> |
46 <param name="idprefix" type="hidden" value="" /> | |
40 <param name="idextension" type="hidden" value="" /> | 47 <param name="idextension" type="hidden" value="" /> |
41 <param name="idlength" type="hidden" value="0" /> | 48 <param name="idlength" type="hidden" value="0" /> |
42 <param name="idcase" type="hidden" value="" /> | 49 <param name="idcase" type="hidden" value="" /> |
43 </when> | 50 </when> |
44 </conditional> | 51 </conditional> |
50 <data format="txt" name="log" label="DBKit Log"> | 57 <data format="txt" name="log" label="DBKit Log"> |
51 <filter>logfile</filter> | 58 <filter>logfile</filter> |
52 </data> | 59 </data> |
53 </outputs> | 60 </outputs> |
54 <tests> | 61 <tests> |
55 <test> | 62 <test expect_num_outputs="2"> |
56 <param name="input" value="create/sequences.tabular" ftype="tabular" /> | 63 <param name="input" value="create/sequences.tabular" ftype="tabular" /> |
57 <param name="inputs" value="create/NP_000282.1.hhr,create/NP_000290.2.hhr,create/NP_000548.2.hhr,create/NP_000836.2.hhr" /> | 64 <param name="inputs" value="create/NP_000282.1.hhr,create/NP_000290.2.hhr,create/NP_000548.2.hhr,create/NP_000836.2.hhr" /> |
58 <conditional name="advanced"> | 65 <conditional name="advanced"> |
59 <param name="type" value="false" /> | 66 <param name="type" value="false" /> |
60 </conditional> | 67 </conditional> |