Mercurial > repos > iracooke > tpp_prophets
comparison protxml_to_table.xml @ 15:0746a2ae9e04 draft
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author | iracooke |
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date | Tue, 20 Oct 2015 20:45:24 -0400 |
parents | d90c8bc10a9c |
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14:d90c8bc10a9c | 15:0746a2ae9e04 |
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1 <tool id="protxml_to_table_1" name="ProtXML to Table" version="1.1.0"> | 1 <tool id="protxml_to_table_1" name="ProtXML to Table" version="1.1.1"> |
2 <requirements> | 2 <description>Converts a ProtXML file to a table</description> |
3 <container type="docker">iracooke/protk-1.4.1</container> | 3 <requirements> |
4 <requirement type="package" version="1.4">protk</requirement> | 4 <container type="docker">iracooke/protk-1.4.3</container> |
5 </requirements> | 5 <requirement type="package" version="1.4.3">protk</requirement> |
6 | 6 </requirements> |
7 <description>Converts a ProtXML file to a table</description> | 7 <command> |
8 | 8 protxml_to_table.rb |
9 <command> | 9 $invert_probs |
10 protxml_to_table.rb | 10 $input_file |
11 $invert_probs | 11 -o $output |
12 | 12 </command> |
13 $input_file | 13 <inputs> |
14 -o $output | 14 <param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/> |
15 </command> | 15 <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> |
16 | 16 </inputs> |
17 <inputs> | 17 <outputs> |
18 | 18 <data format="tabular" name="output" /> |
19 <param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/> | 19 </outputs> |
20 <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> | 20 <tests> |
21 </inputs> | 21 <!-- Just test that the tool runs and produces vaguely correct output --> |
22 | 22 <test> |
23 | 23 <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml" format="protxml"/> |
24 <outputs> | 24 <output name="output" format="tabular"> |
25 <data format="tabular" name="output" /> | 25 <assert_contents> |
26 </outputs> | 26 <has_text text="AVQKYLTAHEQSK" /> |
27 | 27 </assert_contents> |
28 <tests> | 28 </output> |
29 <!-- Just test that the tool runs and produces vaguely correct output --> | 29 </test> |
30 <test> | 30 </tests> |
31 <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml" format="protxml"/> | 31 <help> |
32 <output name="output" format="tabular"> | |
33 <assert_contents> | |
34 <has_text text="AVQKYLTAHEQSK" /> | |
35 </assert_contents> | |
36 </output> | |
37 </test> | |
38 </tests> | |
39 | |
40 | |
41 <help> | |
42 | |
43 **What it does** | 32 **What it does** |
44 | 33 |
45 Converts a ProtXML file to a tab separated table | 34 Converts a ProtXML file to a tab separated table |
46 | 35 |
47 </help> | 36 </help> |
48 | |
49 </tool> | 37 </tool> |