Mercurial > repos > dchristiany > data_manager_proteore_test

annotate data_manager/resource_building.xml @ 3:0902811604a3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
author dchristiany
date Tue, 23 Oct 2018 07:08:35 -0400
parents 80aae68f3481
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
0902811604a3 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents: 2
diff changeset
1 <tool id="data_manager_proteore_test" name="Get source files for proteore tools" version="2018.10.23.3" tool_type="manage_data">
0
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
2 <description>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
3 to create or update reference files for proteore tools
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
4 </description>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
5 <requirements>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
6 </requirements>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
7 <stdio>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
8 <exit_code range="1:" />
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
9 </stdio>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
10 <command><![CDATA[
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
11
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
12 python $__tool_directory__/resource_building.py
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
13 #if $database.database == "human_protein_atlas"
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
14 --hpa "$database.tissues"
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
15 #else if $database.database == "peptide_atlas"
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
16 --peptideatlas "$database.tissues"
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
17 #else if $database.database == "id_mapping"
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
18 --id_mapping="$database.species"
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
19 #end if
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
20 --output "$output"
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
21
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
22 ]]></command>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
23
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
24 <inputs>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
25 <conditional name="database">
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
26 <param name="database" type="select">
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
27 <option value="human_protein_atlas">Human Protein Atlas</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
28 <option value="peptide_atlas">Peptide Atlas</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
29 <option value="id_mapping">ID mapping</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
30 </param>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
31 <when value="human_protein_atlas">
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
32 <param name="tissues" type="select" multiple="false" label="Please select tissue">
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
33 <option value="HPA_normal_tissue">Normal tissue</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
34 <option value="HPA_pathology">Pathology</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
35 <option value="HPA_full_atlas">Full Atlas</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
36 </param>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
37 </when>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
38 <when value="peptide_atlas">
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
39 <param name="tissues" type="select" multiple="false" label="Please select the tissue">
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
40 <option value="1-Human_Liver">Human liver</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
41 <option value="2-Human_Brain">Human brain</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
42 <option value="4-Human_Heart">Human heart</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
43 <option value="5-Human_Kidney">Human kidney</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
44 <option value="10-Human_Plasma">Human blood plasma</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
45 <option value="13-Human_Urine">Human urine</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
46 <option value="24-Human_CSF">Human cerebrospinal fluid</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
47 </param>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
48 </when>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
49 <when value="id_mapping">
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
50 <param name="species" type="select" multiple="false" label="Please select the species">
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
51 <option value="human">Human (Homo sapiens)</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
52 <option value="mouse">Mouse (Mus musculus)</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
53 <option value="rat">Rat (Rattus norvegicus)</option>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
54 </param>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
55 </when>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
56 </conditional>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
57 </inputs>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
58
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
59 <outputs>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
60 <!--data format="tabular" name="output">
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
61 <discover_datasets pattern="(?P&lt;designation&gt;.+).tsv" ext="tabular" visible="true" assign_primary_output="true" />
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
62 </data-->
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
63 <data name="output" format="data_manager_json"/>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
64 </outputs>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
65
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
66 <tests>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
67 </tests>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
68
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
69 <help><![CDATA[
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
70
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
71 TODO
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
72
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
73 -----
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
74
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
75 .. class:: infomark
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
76
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
77 **Authors**
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
78
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
79 Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
80
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
81 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
82
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
83 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
84
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
85 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
86
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
87 ]]></help>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
88 <citations>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
89 </citations>
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
90
55efb19f0b34 planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
dchristiany
parents:
diff changeset
91 </tool>