Mercurial > repos > gga > tripal_expression_add_expression
comparison expression_add_expression.xml @ 0:39b5e6008cbc draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
author | gga |
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date | Mon, 25 Feb 2019 06:20:32 -0500 |
parents | |
children | 9af61a2ba323 |
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-1:000000000000 | 0:39b5e6008cbc |
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1 <?xml version="1.0"?> | |
2 <tool id="expression_add_expression" name="Load expression data" version="@WRAPPER_VERSION@.0"> | |
3 <description>into Tripal</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements"/> | |
8 <code file="tripal.py"/> | |
9 <command detect_errors="aggressive"><![CDATA[ | |
10 tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}" | |
11 | |
12 && | |
13 | |
14 cp '${file_path}' "\${tmp_dir}/expression.tsv" | |
15 | |
16 && | |
17 | |
18 @AUTH@ | |
19 | |
20 tripaille expression add_expression | |
21 '$organism_id' | |
22 '$analysis_id' | |
23 "\${tmp_dir}/expression.tsv" | |
24 | |
25 #if $match_type: | |
26 --match_type '$match_type' | |
27 #end if | |
28 #if $biomaterial_provider: | |
29 --biomaterial_provider '$biomaterial_provider' | |
30 #end if | |
31 #if $array_design: | |
32 --array_design '$array_design' | |
33 #end if | |
34 #if $assay_id: | |
35 --assay_id '$assay_id' | |
36 #end if | |
37 #if $acquisition_id: | |
38 --acquisition_id '$acquisition_id' | |
39 #end if | |
40 #if $quantification_id: | |
41 --quantification_id '$quantification_id' | |
42 #end if | |
43 #if $start_regex: | |
44 --start_regex '$start_regex' | |
45 #end if | |
46 #if $stop_regex: | |
47 --stop_regex '$stop_regex' | |
48 #end if | |
49 | |
50 && | |
51 | |
52 echo "Data loaded" > $results | |
53 ]]></command> | |
54 <inputs> | |
55 <!-- arguments --> | |
56 <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" /> | |
57 <param argument="analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" /> | |
58 <param name="file_path" label="Expression matrix" argument="file_path" type="data" format="tsv,tabular" help="Expression matric (tabular, rows are transcripts, columns are conditions)" /> | |
59 | |
60 <!-- options --> | |
61 <expand macro="match_type" /> | |
62 | |
63 <param name="biomaterial_provider" label="Biomaterial Provider" argument="biomaterial_provider" type="text" help="The contact who provided the biomaterial. (optional, non functional in Tripal2)" optional="true" /> | |
64 | |
65 <param name="array_design" label="Array Design" argument="array_design" type="text" help="The array design associated with this analysis. This is not required if the experimental data was gathered from next generation sequencing methods. (optional, non functional in Tripal2)" optional="true" /> | |
66 | |
67 <param name="assay_id" label="Assay Id" argument="assay_id" type="text" help="The id of the assay associated with the experiment. (optional, non functional in Tripal2)" optional="true" /> | |
68 | |
69 <param name="acquisition_id" label="Acquisition Id" argument="acquisition_id" type="text" help="The id of the acquisition associated with the experiment (optional, non functional in Tripal2)" optional="true" /> | |
70 | |
71 <param name="quantification_id" label="Quantification Id" argument="quantification_id" type="text" help="The id of the quantification associated with the experiment (optional, non functional in Tripal2)" optional="true" /> | |
72 | |
73 <param name="start_regex" label="Start Regex" argument="start_regex" type="text" help="A regular expression to describe the line that occurs before the start of the expression data. If the file has no header, this is not needed. (optional)"> | |
74 <expand macro="sanitized"/> | |
75 </param> | |
76 | |
77 <param name="stop_regex" label="Stop Regex" argument="stop_regex" type="text" help="A regular expression to describe the line that occurs after the end of the expression data. If the file has no footer text, this is not needed. (optional)"> | |
78 <expand macro="sanitized"/> | |
79 </param> | |
80 | |
81 </inputs> | |
82 <outputs> | |
83 <data format="txt" name="results"/> | |
84 </outputs> | |
85 <help> | |
86 :type organism_id: str :param organism_id: Organism Id | |
87 | |
88 @HELP@ | |
89 </help> | |
90 </tool> |